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comparison interpro/paso1.xml @ 0:c342ebb50f0b draft default tip

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author fernando
date Thu, 22 May 2014 05:09:07 -0400
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1 <tool id="ALaGiFer_1" name="RemoteBlast" version="1.0.0">
2 <description>Blast against UniProt/SwissProt database</description>
3 <command interpreter="perl">
4 paso1.pl $infile $outfile
5 </command>
6
7 <inputs>
8 <param name="infile" type="data" format="fasta" label="Sequence in Fasta File"/>
9
10
11 </inputs>
12 <outputs>
13 <data format="txt" name="outfile"/>
14 </outputs>
15
16 <stdio><exit_code range="1:" level="fatal" description="Error" /></stdio>
17 <help>
18
19 **What it does**
20
21 This tool runs a remote blast against Uniprot/Swissprot database.
22
23
24 **Dependencies**
25
26 Bioperl is necessary for running this tool.
27
28 #####
29 Input
30 #####
31
32 Required is a FASTA file containing protein sequences.
33
34
35 ######
36 Output
37 ######
38
39 Generates an output text file.
40
41
42 Example Output
43 --------------
44 BLASTP 2.2.29+
45 Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro
46 A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and
47 David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new
48 generation of protein database search programs", Nucleic
49 Acids Res. 25:3389-3402.
50
51
52 RID: M2E3HVH4014
53
54
55 Database: Non-redundant UniProtKB/SwissProt sequences
56 457,803 sequences; 170,956,615 total letters
57 Query= C08B11.6 CE30856 WBGene00007434 actin status:Confirmed
58 UniProt:Q09443 protein_id:CAA86667.3
59
60 Length=418
61
62
63 Score E
64 Sequences producing significant alignments: (Bits) Value
65
66 sp|Q09443.3|ARP6_CAEEL RecName: Full=Actin-like protein C08B11.6 853 0.0
67 sp|Q9D864.2|ARP6_MOUSE RecName: Full=Actin-related protein 6;... 280 2e-88
68 sp|Q9GZN1.1|ARP6_HUMAN RecName: Full=Actin-related protein 6;... 279 5e-88
69 sp|Q9DEE9.1|ARP6_CHICK RecName: Full=Actin-related protein 6;... 274 5e-86
70 sp|P45890.1|ARP6_DROME RecName: Full=Actin-related protein 6;... 265 1e-82
71 sp|Q6C982.1|ARP6_YARLI RecName: Full=Actin-like protein ARP6 232 4e-70
72 sp|O94241.1|ARP6_SCHPO RecName: Full=Actin-like protein arp6 228 2e-68
73 sp|Q7S6X6.1|ARP6_NEUCR RecName: Full=Actin-related protein 6 212 6e-62
74 sp|Q5NBI2.1|ARP6_ORYSJ RecName: Full=Actin-related protein 6 ... 210 3e-61
75
76 ALIGNMENTS
77 >sp|Q09443.3|ARP6_CAEEL RecName: Full=Actin-like protein C08B11.6
78 Length=418
79
80 Score = 853 bits (2204), Expect = 0.0
81 Identities = 418/418 (100%), Positives = 418/418 (100%), Gaps = 0/418 (0%)
82
83 Query 1 MSLTTIIFDNGGHNMKIGTIDSESPRLVPNSIVKAKHEKKRVFVAHEQEECSDKFSLFYV 60
84 MSLTTIIFDNGGHNMKIGTIDSESPRLVPNSIVKAKHEKKRVFVAHEQEECSDKFSLFYV
85 Sbjct 1 MSLTTIIFDNGGHNMKIGTIDSESPRLVPNSIVKAKHEKKRVFVAHEQEECSDKFSLFYV 60
86
87 Query 61 RPIERGYVVNWDTQQQIWEKTFGSMDVEASTSRIALTDNNYLIPALPDVSSEILFDYFGF 120
88 RPIERGYVVNWDTQQQIWEKTFGSMDVEASTSRIALTDNNYLIPALPDVSSEILFDYFGF
89 Sbjct 61 RPIERGYVVNWDTQQQIWEKTFGSMDVEASTSRIALTDNNYLIPALPDVSSEILFDYFGF 120
90
91 Query 121 TEVHKTSASTLVAKHSNKINNEKCAVVVDSGFSWTTVASFVNGMLIQDSVIRIDVGGKAL 180
92 TEVHKTSASTLVAKHSNKINNEKCAVVVDSGFSWTTVASFVNGMLIQDSVIRIDVGGKAL
93 Sbjct 121 TEVHKTSASTLVAKHSNKINNEKCAVVVDSGFSWTTVASFVNGMLIQDSVIRIDVGGKAL 180
94
95 Query 181 TNKLKDWVSYRQLNVSEETYVINECKEDLCFVSQNFDESMKEARNRFQENTTMKRYIMPD 240
96 TNKLKDWVSYRQLNVSEETYVINECKEDLCFVSQNFDESMKEARNRFQENTTMKRYIMPD
97 Sbjct 181 TNKLKDWVSYRQLNVSEETYVINECKEDLCFVSQNFDESMKEARNRFQENTTMKRYIMPD 240
98
99
100 **Galaxy Wrapper Authors**::
101
102 * Laura Entrambasaguas
103 * Ginés Almagro
104 * Fernando Pérez
105
106 </help>
107 </tool>