In this tutorial we will show how to use the command-line server scripts to download all the genes for a genome.
To get a list of all the features in a genome, use svr_genome_functions and specify the genome ID. The following command lists all the features for genome 360108.3.
svr_genome_functions 360108.3 >genes.tbl
The output will be a tab-delimited file, with the FIG feature ID in the first column, a location string in the second column, and the text of the functional assignment in the third.
fig|360108.3.peg.1 360108.3:NZ_AANK01000008_3178-720 Putative periplasmic ATP /GTP-binding protein fig|360108.3.peg.10 360108.3:NZ_AANK01000008_9127+210 Putative H-T-H containing protein fig|360108.3.peg.100 360108.3:NZ_AANK01000005_2781+978 Putative periplasmic protein fig|360108.3.peg.1000 360108.3:NZ_AANK01000002_231249+804 Zinc ABC transporter, inner membrane permease protein ZnuB fig|360108.3.peg.1001 360108.3:NZ_AANK01000002_232319-279 hypothetical protein fig|360108.3.peg.1002 360108.3:NZ_AANK01000002_233051-711 DNA modification methyltransferase (EC 2.1.1.-) fig|360108.3.peg.1003 360108.3:NZ_AANK01000002_233515-468 DNA-cytosine methyltransferase (EC 2.1.1.37) fig|360108.3.peg.1004 360108.3:NZ_AANK01000002_234102-564 Cytosine-specific DNA methyltransferase fig|360108.3.peg.1005 360108.3:NZ_AANK01000002_234878-780 MnlI restriction endonuclease fig|360108.3.peg.1006 360108.3:NZ_AANK01000002_235273-387 hypothetical protein fig|360108.3.peg.1007 360108.3:NZ_AANK01000002_235696-423 COG0779: clustered with transcription termination protein NusA fig|360108.3.peg.1008 360108.3:NZ_AANK01000002_236048-363 Ribosome-binding factor A fig|360108.3.peg.1009 360108.3:NZ_AANK01000002_238627-2583 Translation initiation factor 2 fig|360108.3.peg.101 360108.3:NZ_AANK01000005_3759+987 Alanine racemase (EC 5.1.1.1) fig|360108.3.peg.1010 360108.3:NZ_AANK01000002_238811-198 Hypothetical protein Cj0135 fig|360108.3.peg.1011 360108.3:NZ_AANK01000002_239774-879 Homoserine kinase (EC 2.7.1.39)
The svr_fasta command can be used to get the DNA for the genes in FASTA form. Normally, svr_fasta takes its input from the last column. Since the FIG ID is in the first column of the output from svr_genome_functions, we use the --c=1 option on the command line.
svr_genome_functions 360108.3 | svr_fasta --c=1 --fasta
The location string and function will be included as comments on the FASTA output, as shown below.
>fig|360108.3.peg.1 360108.3:NZ_AANK01000008_3178-720 Putative periplasmic ATP /GTP-binding protein ttgttagaatttgtgtttataattcttattttaggtatagtttttaatttaggtagtctt tacttaaaaaaagacaatttactagaaggcgcaatacaaattcttaatgatatccaatat acccaaagtttagccatgatgcaagaaggtataagagttgatgagttggctatcgcaaaa agagagtggtttaaaagtaggtggcagatttattttataaaatcagctgccacaggttat gatcaaacatatactattttcttggataaaaatggcgatggaaatgctaatttaggtaaa actgaaatcaatatagatagagaaattgctgttgatgtaatcaatcataacaaattaatg aattcaggtcaaagtggagttattagtaaagatgatgaaaaaactacacaaagatttaat cttacaaaaagattcggaatagaaaaggttgaattcaaaggatcttgttcaggatttact agattagtatttgatgaaatgggcagagtatattctccgttaaaaaatgccaattatgcc tatgaaaaaactttagcaaagaataattcagattgcattatacgtttgttatcaaaaaag catgctctttgtatcgttatagatacgcttagtggttatgcttatattccagattttaaa acacttaaaagtcaatttgttaatataaaaaataaaaattacgagtgctctaaaatataa >fig|360108.3.peg.10 360108.3:NZ_AANK01000008_9127+210 Putative H-T-H containing protein atgacaaaaaagagcaagcgtgatatggcatatgaactagacattgatgttagcacttta tataattggagaaaatataaacccaatttatatcgtattgttatgcttggctttaaattt gatgaacttttagaaaatagcaaaaaaactcatgaagaattgcttcatatagaacaaact atacaagatgagattgctaaatttaaataa >fig|360108.3.peg.100 360108.3:NZ_AANK01000005_2781+978 Putative periplasmic protein ttgttaaaacgacttgctttattaattacactttcttcattgatattgcatgcctcagat cttgttaaaatttatcttaatcaaggattagatgctgttggtgtagcgattgaaaaagaa ttaactcaaaagggtttttggttaagtgaaataggagataaaaatatttcacttggatac tatgatgataatgttgctatcgtgcttacaaataaaacagataaaattcttcgtgtttat tcttatgaggacggaaaaataagaaaagattttgaacaaaaagaaataataactggatta atgggcgataaaaaaatagaaggagatttgaaaacgccagtaggtttttatgagttaggc cgtaagtttaacccaggtgatccttattatggtccctttgcttttgctacaacttatcca aatttacttgataaagtacaaggaaaaacaggtggtggtatttggatccatggctatcct ttagatggttctagacttgatgaatttaaaacaagagggtgtattgctttatttaataat aatttggagaaatttgcacaagttgtacaagataaaaaagtttttgttatgacagaagaa aaagaaaaaattagagctaaaaaggatcaaatagctagtttattggctgatctttttaca tggaaactagcttggacaaatagtgacactaatacctatttaagtttttatgatgagcaa gaatttaaacgttttgataaaatgaaatttgaacagtttgcttccatgaaaaaatctatt ttttctcgtaaagaagataaaaagattaaattttcagatattaatatcagcccttatccg aatttagaaaatgaaactatgtatagaatttcattttatgaggattattacactaaaaac tatcagtttagaggcgataaaattttatacgttaagatagatagtaaaggtaaaatgaaa attttagcagagcaataa
