# HG changeset patch # User jamueller # Date 1558602908 14400 # Node ID caadae802e656f7c71ceb1f838c3c4e8a2195fd7 Uploaded diff -r 000000000000 -r caadae802e65 gcs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gcs.xml Thu May 23 05:15:08 2019 -0400 @@ -0,0 +1,118 @@ + + (GeneCodonSearch) calculates the codon composition in a DNA sequence. + GeneCodonSearch1_2.py -c $codon -m $minimum -i $input_sequences -r $resultfile + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + **What it does** + **GeCos** is a tool that calculates the codon composition of any given DNA sequence. + + **Input** + + - If more than one sequence is analyzed at a time, a **cutoff value** can be used to filter the output. Only the sequences with a higher total score than the cutoff value will be displayed in the output. + + - The DNA sequence(s), that are supposed to be analyzed with GeCoS need to be formatted as fasta. + + Example:: + + >CCE57618 cdna plasmid:HUSEC2011CHR1:pHUSEC2011-2:166:1143:1 gene:HUS2011_pII0001 description:replication initiation protein RepFIB + GTGGATAAGTC ... TCTTCAAATCCCGCTGA + >CCE57620 cdna plasmid:HUSEC2011CHR1:pHUSEC2011-2:1422:2162:-1 gene:HUS2011_pII0003 description:site-specific recombinase + ATGAACAATG ... CTCCCCTGAAGTAA + >CCE57621 cdna plasmid:HUSEC2011CHR1:pHUSEC2011-2:2531:2692:-1 gene:HUS2011_pII0004 description:plasmid stabilisation system family protein + ATGAGTAATCA ... ATTTCAACTGA + >CCE57622 cdna plasmid:HUSEC2011CHR1:pHUSEC2011-2:2894:3076:-1 gene:HUS2011_pII0005 description:putative transcriptional regulator + ATGGCCAG ... AGAAGGCT + + **Output** + + - GeCoS produces a matrix containing the identifier used in the input, the combined score of the sequence and the number of each of the chosen codons. + + - **Total Score** = sum of codon occurences / sequence length * number of analyzed codons + + - The output is sorted from low to high (Total Score: 0 to 1). + + Example:: + + [['Gene_ID' 'Total Score' 'AGG' 'AGC' 'CCC' 'TGC' 'GCG'] + ['CCE57562' 0.0190476 1 3 1 2 1] + ['CCQ29559' 0.0190476 0 1 2 2 1] + ... + ['CCQ31238' 0.0328358 0 3 0 6 2] + ['CCE57539' 0.05 2 0 4 3 3]] + + + +