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1 genret
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2 Function
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3
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4 Retrieves various gene related information from genome flatfile
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5
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6 Description
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7
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8 genret reads in one or more genome flatfiles and retrieves various data from
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9 the input file. It is a wrapper program to the G-language REST service,
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10 where a method is specified by giving a string to the "method" qualifier. By
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11 default, genret will parse the input file to retrieve the accession ID
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12 (or name) of the genome to query G-language REST service. By setting the
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13 "accid" qualifier to false (or 0), genret will instead parse the sequence
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14 and features of the genome to create a GenBank formatted flatfile and upload
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15 the file to the G-language web server. Using the file uploaded, genret will
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16 execute the method provided.
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17
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18 genret is able to perform a variety of tasks, incluing the retrieval of
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19 sequence upstream, downstream, or around the start or stop codon,
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20 translated gene sequences search of gene data by keyword, and re-annotation
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21 and retrieval of genome flatfiles. The set of genes can be given as flat
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22 text, regular expression, or a file containing the list of genes.
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23
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24 Details on G-language REST service is available from the wiki page
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25
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26 http://www.g-language.org/wiki/rest
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27
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28 Documentation on G-language Genome Analysis Environment methods are
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29 provided at the Document Center
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30
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31 http://ws.g-language.org/gdoc/
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32
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33 Usage
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34
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35 Here is a sample session with genret
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36
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37 Retrieving sequences upstream, downstream, or around the start/stop codons.
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38 The following example shows the retrieval of sequence around the start
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39 codons of all genes.
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40
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41 Genes to access are specified by regular expression. '*' stands for every
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42 gene.
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43
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44 Available methods are:
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45 after_startcodon
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46 after_stopcodon
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47 around_startcodon
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48 around_stopcodon
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49 before_startcodon
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50 before_stopcodon
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51
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52 % genret
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53 Retrieves various gene related information from genome flatfile
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54 Input nucleotide sequence(s): refseqn:NC_000913
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55 Gene name(s) to lookup [*]:
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56 Feature to access: around_startcodon
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57 Full text output file [nc_000913.around_startcodon]:
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58
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59 Go to the input files for this example
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60 Go to the output files for this example
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61
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62 Example 2
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63
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64 Using flat text as target genes. The names can be split with with a space,
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65 comma, or vertical bar.
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66
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67 % genret
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68 Retrieves various gene related information from genome flatfile
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69 Input nucleotide sequence(s): refseqn:NC_000913
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70 List of gene name(s) to report [*]: recA,recB
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71 Name of gene feature to access: translation
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72 Sequence output file [nc_000913.translation.genret]: stdout
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73 >recA
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74 MAIDENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALGAGGLPMGR
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75 IVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDT
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76 GEQALEICDALARSGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGNL
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77 KQSNTLLIFINQIRMKIGVMFGNPETTTGGNALKFYASVRLDIRRIGAVKEGENVVGSETR
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78 VKVVKNKIAAPFKQAEFQILYGEGINFYGELVDLGVKEKLIEKAGAWYSYKGEKIGQGKAN
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79 ATAWLKDNPETAKEIEKKVRELLLSNPNSTPDFSVDDSEGVAETNEDF
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80 >recB
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81 MSDVAETLDPLRLPLQGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLV
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82 VTFTEAATAELRGRIRSNIHELRIACLRETTDNPLYERLLEEIDDKAQAAQWLLLAERQMD
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83 EAAVFTIHGFCQRMLNLNAFESGMLFEQQLIEDESLLRYQACADFWRRHCYPLPREIAQVV
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84 FETWKGPQALLRDINRYLQGEAPVIKAPPPDDETLASRHAQIVARIDTVKQQWRDAVGELD
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85 ALIESSGIDRRKFNRSNQAKWIDKISAWAEEETNSYQLPESLEKFSQRFLEDRTKAGGETP
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86 RHPLFEAIDQLLAEPLSIRDLVITRALAEIRETVAREKRRRGELGFDDMLSRLDSALRSES
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87 GEVLAAAIRTRFPVAMIDEFQDTDPQQYRIFRRIWHHQPETALLLIGDPKQAIYAFRGADI
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88 FTYMKARSEVHAHYTLDTNWRSAPGMVNSVNKLFSQTDDAFMFREIPFIPVKSAGKNQALR
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89 FVFKGETQPAMKMWLMEGESCGVGDYQSTMAQVCAAQIRDWLQAGQRGEALLMNGDDARPV
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90 RASDISVLVRSRQEAAQVRDALTLLEIPSVYLSNRDSVFETLEAQEMLWLLQAVMTPEREN
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91 TLRSALATSMMGLNALDIETLNNDEHAWDVVVEEFDGYRQIWRKRGVMPMLRALMSARNIA
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92 ENLLATAGGERRLTDILHISELLQEAGTQLESEHALVRWLSQHILEPDSNASSQQMRLESD
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93 KHLVQIVTIHKSKGLEYPLVWLPFITNFRVQEQAFYHDRHSFEAVLDLNAAPESVDLAEAE
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94 RLAEDLRLLYVALTRSVWHCSLGVAPLVRRRGDKKGDTDVHQSALGRLLQKGEPQDAAGLR
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95 TCIEALCDDDIAWQTAQTGDNQPWQVNDVSTAELNAKTLQRLPGDNWRVTSYSGLQQRGHG
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96 IAQDLMPRLDVDAAGVASVVEEPTLTPHQFPRGASPGTFLHSLFEDLDFTQPVDPNWVREK
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97 LELGGFESQWEPVLTEWITAVLQAPLNETGVSLSQLSARNKQVEMEFYLPISEPLIASQLD
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98 TLIRQFDPLSAGCPPLEFMQVRGMLKGFIDLVFRHEGRYYLLDYKSNWLGEDSSAYTQQAM
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99 AAAMQAHRYDLQYQLYTLALHRYLRHRIADYDYEHHFGGVIYLFLRGVDKEHPQQGIYTTR
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100 PNAGLIALMDEMFAGMTLEEA
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101
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102 Example 3
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103
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104 Using a file with a list of gene names.
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105 The following example will retrieve the strand direction for each gene
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106 listed in the "gene_list.txt" file. String prefixed with an "@" or "list::"
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107 will be interpreted as file names.
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108
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109 % genret
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110 Retrieves various gene features from genome flatfile
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111 Input nucleotide sequence(s): refseqn:NC_000913
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112 List of gene name(s) to report [*]: @gene_list.txt
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113 Name of gene feature to access: direction
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114 Full text output file [nc_000913.direction]: stdout
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115 gene,direction
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116 thrA,direct
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117 thrB,direct
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118 thrC,direct
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119
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120 Go to the input files for this example
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121 Go to the output files for this example
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122
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123 Example 4
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124
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125 Retrieving translations of coding sequences.
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126 The following example will retrieve the translated protein sequence of
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127 the "recA" gene.
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128
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129 % genret
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130 Retrieves various gene related information from genome flatfile
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131 Input nucleotide sequence(s): refseqn:NC_000913
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132 Gene name(s) to lookup [*]: recA
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133 Feature to access: translation
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134 Full text output file [nc_000913.translation]: stdout
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135 >recA
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136 MAIDENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALGAGGLPMGR
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137 IVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDT
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138 GEQALEICDALARSGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGNL
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139 KQSNTLLIFINQIRMKIGVMFGNPETTTGGNALKFYASVRLDIRRIGAVKEGENVVGSETR
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140 VKVVKNKIAAPFKQAEFQILYGEGINFYGELVDLGVKEKLIEKAGAWYSYKGEKIGQGKAN
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141 ATAWLKDNPETAKEIEKKVRELLLSNPNSTPDFSVDDSEGVAETNEDF
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142
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143 Example 5
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144
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145 Retrieving feature information of the genes.
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146 The following example will retrieve the start positions for each gene.
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147 The values for the keys in GenBank format is available for retrieval.
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148 (ex. start end direction GO* etc.)
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149 Positions will be returned with a 1 start value.
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150
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151 % genret
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152 Retrieves various gene related information from genome flatfile
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153 Input nucleotide sequence(s): refseqn:NC_000913
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154 Gene name(s) to lookup [*]:
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155 Feature to access: start
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156 Full text output file [nc_000913.start]:
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157
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158 Go to the input files for this example
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159 Go to the output files for this example
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160
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161 Example 6
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162
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163 Passing extra arguments to the methods.
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164 The following example shows the retrieval of 30 base pairs around the
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165 start codon of the "recA" gene. By default, the "around_startcodon" method
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166 returns 200 base pairs around the start codon. Using the "-argument"
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167 qualifier allows the user to change this value.
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168
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169 % genret refseqn:NC_000913 recA around_startcodon -argument 30,30 stdout
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170 Retrieves various gene features from genome flatfile
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171 >recA
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172 ccggtattacccggcatgacaggagtaaaaatggctatcgacgaaaacaaacagaaagcgt
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173 tg
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174
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175 Example 7
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176
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177 Re-annotating a flatfile.
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178 genret supports re-annotation of a genome flatfile via Restauro-G
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179 service developed by our team. Using the BLAST Like Alignment Tool,
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180 to refer the UniProt KB and annotates information including the description,
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181 comments, feature tables, cross references, COG family, position, and Pfam.
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182 The original software is available at [http://restauro-g.iab.keio.ac.jp].
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183
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184
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185 % genret refseqn:NC_000913 '*' annotate nc_000913-annotate.gbk
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186 Retrieves various gene features from genome flatfile
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187
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188 Command line arguments
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189
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190 Standard (Mandatory) qualifiers:
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191 [-sequence] seqall Nucleotide sequence(s) filename and optional
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192 format, or reference (input USA)
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193 [-gene] string [*] Gene name(s) to lookup (Any string)
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194 [-access] string Feature to access (Any string)
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195 [-outfile] outfile [*.genret] Full text output file
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196
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197 Additional (Optional) qualifiers: (none)
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198 Advanced (Unprompted) qualifiers:
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199 -argument string Option to give to method (Any string)
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200 -[no]accid boolean [Y] Include to use sequence accession ID as
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201 query
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202
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203 General qualifiers:
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204 -help boolean Report command line options and exit. More
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205 information on associated and general
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206 qualifiers can be found with -help -verbose
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207
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208 Input file format
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209
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210 Database definitions for the examples are included in the embossrc_template
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211 file of the Keio Bioinformatcs Web Service (KBWS) package.
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212
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213 Input files for usage example 4
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214
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215 File: gene_list.txt
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216
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217 thrA
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218 thrB
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219 thrC
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220
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221 Output file format
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222
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223 Output files for usage example 1
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224
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225 File: nc_000913.around_startcodon
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226
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227 >thrL
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228 cgtgagtaaattaaaattttattgacttaggtcactaaatactttaaccaatataggcata
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229 gcgcacagacagataaaaattacagagtacacaacatccatgaaacgcattagcaccacca
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230 ttaccaccaccatcaccattaccacaggtaacggtgcgggctgacgcgtacaggaaacaca
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231 gaaaaaagcccgcacctgac
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232 >thrA
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233 aggtaacggtgcgggctgacgcgtacaggaaacacagaaaaaagcccgcacctgacagtgc
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234 gggctttttttttcgaccaaaggtaacgaggtaacaaccatgcgagtgttgaagttcggcg
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235 gtacatcagtggcaaatgcagaacgttttctgcgtgttgccgatattctggaaagcaatgc
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236 caggcaggggcaggtggcca
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237
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238 [Part of this file has been deleted for brevity]
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239
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240 >yjjY
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241 tgcatgtttgctacctaaattgccaactaaatcgaaacaggaagtacaaaagtccctgacc
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242 tgcctgatgcatgctgcaaattaacatgatcggcgtaacatgactaaagtacgtaattgcg
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243 ttcttgatgcactttccatcaacgtcaacaacatcattagcttggtcgtgggtactttccc
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244 tcaggacccgacagtgtcaa
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245 >yjtD
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246 tttttctgcgacttacgttaagaatttgtaaattcgcaccgcgtaataagttgacagtgat
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247 cacccggttcgcggttatttgatcaagaagagtggcaatatgcgtataacgattattctgg
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248 tcgcacccgccagagcagaaaatattggggcagcggcgcgggcaatgaaaacgatggggtt
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249 tagcgatctgcggattgtcg
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250
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251 Output files for usage example 5
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252
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253 File: nc_000913.start
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254
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255 gene,start
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256 thrL,190
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257 thrA,337
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258 thrB,2801
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259 thrC,3734
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260 yaaX,5234
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261 yaaA,5683
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262 yaaJ,6529
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263 talB,8238
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264 mog,9306
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265
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266 [Part of this file has been deleted for brevity]
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267
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268 yjjX,4631256
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269 ytjC,4631820
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270 rob,4632464
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271 creA,4633544
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272 creB,4634030
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273 creC,4634719
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274 creD,4636201
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275 arcA,4637613
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276 yjjY,4638425
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277 yjtD,4638965
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278
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279 Output files for usage example 7
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280
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281 File: ecoli-annotate.gbk
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282
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283 LOCUS NC_000913 4639675 bp DNA circular BCT 25-OCT-2010
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284 DEFINITION Escherichia coli str. K-12 substr. MG1655 chromosome, complete
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285 genome.
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286 ACCESSION NC_000913
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287 VERSION NC_000913.2 GI:49175990
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288 DBLINK Project: 57779
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289 KEYWORDS .
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290 SOURCE Escherichia coli str. K-12 substr. MG1655
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291 ORGANISM Escherichia coli str. K-12 substr. MG1655
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292 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
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293
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294 [Part of this file has been deleted for brevity]
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295
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296 CDS 2801..3733
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297 /EC_number="2.7.1.39"
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298 /codon_start="1"
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299 /db_xref="GI:16127997"
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300 /db_xref="ASAP:ABE-0000010"
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301 /db_xref="UniProtKB/Swiss-Prot:P00547"
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302 /db_xref="ECOCYC:EG10999"
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303 /db_xref="EcoGene:EG10999"
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304 /db_xref="GeneID:947498"
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305 /function="enzyme; Amino acid biosynthesis: Threonine"
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306 /function="1.5.1.8 metabolism; building block
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307 biosynthesis; amino acids; threonine"
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308 /function="7.1 location of gene products; cytoplasm"
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309 /gene="thrB"
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310 /gene_synonym="ECK0003; JW0002"
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311 /locus_tag="b0003"
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312 /note="GO_component: GO:0005737 - cytoplasm; GO_process:
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313 GO:0009088 - threonine biosynthetic process"
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314 /product="homoserine kinase"
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315 /protein_id="NP_414544.1"
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316 /rs_com="FUNCTION: Catalyzes the ATP-dependent
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317 phosphorylation of L- homoserine to L-homoserine
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318 phosphate (By similarity)."
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319 /rs_com="CATALYTIC ACTIVITY: ATP + L-homoserine = ADP +
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320 O-phospho-L- homoserine."
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321 /rs_com="PATHWAY: Amino-acid biosynthesis; L-threonine
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322 biosynthesis; L- threonine from L-aspartate: step 4/5."
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323 /rs_com="SUBCELLULAR LOCATION: Cytoplasm (Potential)."
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324 /rs_com="SIMILARITY: Belongs to the GHMP kinase family.
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325 Homoserine kinase subfamily."
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326 /rs_des="RecName: Full=Homoserine kinase; Short=HK;
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327 Short=HSK; EC=2.7.1.39;"
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328 /rs_protein="Level 1: similar to KHSE_ECODH 1.7e-180"
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329 /rs_xr="EMBL; CP000948; ACB01208.1; -; Genomic_DNA."
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330 /rs_xr="RefSeq; YP_001728986.1; -."
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331 /rs_xr="ProteinModelPortal; B1XBC8; -."
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332 /rs_xr="SMR; B1XBC8; 2-308."
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333 /rs_xr="EnsemblBacteria; EBESCT00000012034;
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334 EBESCP00000011562; EBESCG00000011096."
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335 /rs_xr="GeneID; 6058639; -."
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336 /rs_xr="GenomeReviews; CP000948_GR; ECDH10B_0003."
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337 /rs_xr="KEGG; ecd:ECDH10B_0003; -."
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338 /rs_xr="HOGENOM; HBG646290; -."
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339 /rs_xr="OMA; GSAHADN; -."
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340 /rs_xr="ProtClustDB; PRK01212; -."
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341 /rs_xr="BioCyc; ECOL316385:ECDH10B_0003-MONOMER; -."
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342 /rs_xr="GO; GO:0005737; C:cytoplasm;
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343 IEA:UniProtKB-SubCell."
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344 /rs_xr="GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW."
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345 /rs_xr="GO; GO:0004413; F:homoserine kinase activity;
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346 IEA:EC."
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347 /rs_xr="GO; GO:0009088; P:threonine biosynthetic process;
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348 IEA:UniProtKB-KW."
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349 /rs_xr="HAMAP; MF_00384; Homoser_kinase; 1; -."
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350 /rs_xr="InterPro; IPR006204; GHMP_kinase."
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351 /rs_xr="InterPro; IPR013750; GHMP_kinase_C."
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352 /rs_xr="InterPro; IPR006203; GHMP_knse_ATP-bd_CS."
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353 /rs_xr="InterPro; IPR000870; Homoserine_kin."
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354 /rs_xr="InterPro; IPR020568; Ribosomal_S5_D2-typ_fold."
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355 /rs_xr="InterPro; IPR014721;
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356 Ribosomal_S5_D2-typ_fold_subgr."
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357 /rs_xr="Gene3D; G3DSA:3.30.230.10;
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358 Ribosomal_S5_D2-type_fold; 1."
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359 /rs_xr="Pfam; PF08544; GHMP_kinases_C; 1."
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360 /rs_xr="Pfam; PF00288; GHMP_kinases_N; 1."
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361 /rs_xr="PIRSF; PIRSF000676; Homoser_kin; 1."
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362 /rs_xr="PRINTS; PR00958; HOMSERKINASE."
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363 /rs_xr="SUPFAM; SSF54211; Ribosomal_S5_D2-typ_fold; 1."
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364 /rs_xr="TIGRFAMs; TIGR00191; thrB; 1."
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365 /rs_xr="PROSITE; PS00627; GHMP_KINASES_ATP; 1."
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366 /transl_table="11"
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367 /translation="MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETF
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368 SLNNLGRFADKLPSEPRENIVYQCWERFCQELGKQIPVAMTLEKNMPIGSGLGSSACS
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369 VVAALMAMNEHCGKPLNDTRLLALMGELEGRISGSIHYDNVAPCFLGGMQLMIEENDI
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370 ISQQVPGFDEWLWVLAYPGIKVSTAEARAILPAQYRRQDCIAHGRHLAGFIHACYSRQ
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371 PELAAKLMKDVIAEPYRERLLPGFRQARQAVAEIGAVASGISGSGPTLFALCDKPETA
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372 QRVADWLGKNYLQNQEGFVHICRLDTAGARVLEN"
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373
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374 [Part of this file has been deleted for brevity]
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375
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376 4639201 gcgcagtcgg gcgaaatatc attactacgc cacgccagtt gaactggtgc cgctgttaga
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377 4639261 ggaaaaatct tcatggatga gccatgccgc gctggtgttt ggtcgcgaag attccgggtt
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378 4639321 gactaacgaa gagttagcgt tggctgacgt tcttactggt gtgccgatgg tggcggatta
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379 4639381 tccttcgctc aatctggggc aggcggtgat ggtctattgc tatcaattag caacattaat
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380 4639441 acaacaaccg gcgaaaagtg atgcaacggc agaccaacat caactgcaag ctttacgcga
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381 4639501 acgagccatg acattgctga cgactctggc agtggcagat gacataaaac tggtcgactg
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382 4639561 gttacaacaa cgcctggggc ttttagagca acgagacacg gcaatgttgc accgtttgct
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383 4639621 gcatgatatt gaaaaaaata tcaccaaata aaaaacgcct tagtaagtat ttttc
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384 //
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385
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386 Data files
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387
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388 None.
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389
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390 Notes
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391
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392 None.
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393
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394 References
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395
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396 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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397 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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398 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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399
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400 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
|
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401 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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402 31, 7.
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403
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404 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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405 Analysis Environment with REST and SOAP Web Service Interfaces,
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406 Nucleic Acids Res., 38, W700-W705.
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407
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408 Warnings
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409
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410 None.
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411
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412 Diagnostic Error Messages
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413
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414 None.
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415
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416 Exit status
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417
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418 It always exits with a status of 0.
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419
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420 Known bugs
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421
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422 None.
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423
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424 See also
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425
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426 entret Retrieve sequence entries from flatfile databases and files
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427 seqret Read and write (return) sequences
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428
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429 Author(s)
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430
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431 Hidetoshi Itaya (celery@g-language.org)
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432 Institute for Advanced Biosciences, Keio University
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433 252-0882 Japan
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434
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435 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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436 Institute for Advanced Biosciences, Keio University
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437 252-0882 Japan
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438
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439 History
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440
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441 2012 - Written by Hidetoshi Itaya
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442
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443 Target users
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444
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445 This program is intended to be used by everyone and everything, from
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446 naive users to embedded scripts.
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447
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448 Comments
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449
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450 None.
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451
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