WGS Example Files

Remember that the columns in a .tbl file must be tab-delimited. If the samples in which the complete sequence is included do not work, check that tabs separate the columns, not spaces.

• Simple file
• Multiple sequences in a file
• Partial coding regions
• Features on the complementary strand

Simple file

sample.fsa

>Cont54 [organism=Homo sapiens] [chromosome=5]
acaagcgctgctgtcgatgcaaactttagcttttaaacaagtgcaaacgcacgctgtctc
acatgataacacacattatcagaatactttccatgcaatatgaaaccatagcaagctacg
....

sample.tbl

>Features Cont54
10400   12512   gene
            locus_tag   CCC_03116
10400   10462   mRNA
10533   10577
10651   11098
11182   11642
11716   12512
            product aldolase
            protein_id  gnl|dbname|CCC_03116
            transcript_id   gnl|dbname|mrna.CCC_03116
10450   10462   CDS
10533   10577
10651   11098
11182   11642
11716   12233
            product aldolase
            protein_id  gnl|dbname|CCC_03116
            transcript_id   gnl|dbname|mrna.CCC_03116
            inference   profile:Genscan:2.0
15801   17688   gene
            locus_tag   CCC_03118
15801   16607   mRNA
16750   17688
            product hypothetical protein
            protein_id  gnl|dbname|CCC_03118
            transcript_id   gnl|dbname|mrna.CCC_03118
15840   16607   CDS
16750   17610
            product hypothetical protein
            protein_id  gnl|dbname|CCC_03118
            transcript_id   gnl|dbname|mrna.CCC_03118
            inference   similar to RNA sequence, mRNA:INSD:AY123456.2



Here is the definition line of the flatfile view of the final record made
with these files:

DEFINITION  Homo sapiens chromosome 5 Cont54, whole genome shotgun sequence.

Files for multiple sequences

multiple.fsa

>Cont348.225 [organism=Helicobacter pylori ABC1] [strain=ABC1] [host=Homo sapiens] [isolation-source=blood]
TTGAAGCAAGGCATTAGGCGAACCACTGCCTCTCTTTTACCTTCTTTTTTTTCCACCATTATTACTTTACTTTACATACGTTTAGGATCTGG
CGAGCAGCCCAGGCGAGTGTTTTGTAGTTTTCTCGGGGCTGCCTTTTTTTCTCTCTGTGGATGTGTGTGTGGGTATGGGCTGTATTTTCCTG
>Cont442.125 [organism=Helicobacter pylori ABC1] [strain=ABC1] [host=Homo sapiens] [isolation-source=blood]
TTGAAGCAAGGCATTAGGCGAACCACTGCCTCTCTTTTACCTTCTTTTTTTTCCACCATTATTACTTTACTTTACATACGTTTAGGATCTGG
CGAGCAGCCCAGGCGAGTGTTTTGTAGTTTTCTCGGGGCTGCCTTTTTTTCTCTCTGTGGATGTGTGTGTGGGTATGGGCTGTATTTTCCTG


multiple.tbl

>Features Cont348.225
11  109 gene
            locus_tag   HPC_002564
            gene    cheA
11  109 CDS
            product CheA
            protein_id  gnl|dbname|HPC_002564
>Features Cont442.125
15  113 gene
            locus_tag   HPC_003020
15  113 CDS
            product TPR repeat-containing protein
            protein_id  gnl|dbname|HPC_003020
            experiment  Northern blot

Partial coding region

The first coding region is partial at the 5' end and nucleotide 3 is the beginning of the first complete codon. Therefore, " < " indicates 5' partial, and codon_start "3" indicates the start of the first codon.

The second coding region is partial at the 3' end, so " > " is used to indicate 3' partial.

partial.fsa

>Cont3  [organism=Mus musculus] [strain=BALB/c] [chromosome=2]
TGcaaagtGGAATTCCAATTTCAACACCAGTTTTTGATGGCGCAAAAGAGCAAGATGTAACAAATATGTTAGAGCTTGCATCATTACCAAAATCTGG
TCAAACAAAATTGTGGGATGGTAGAACAGGTGAAAAATTTGATAGAGAAGTCACAGTTGGCACTATTTATATGTTAAAATTACACCATCTTGTAGAA
GATAAAATACACGCAAGATCTACAGGTCCTTATAGTTTAGTTACACAACAACCTCTTGGTGGTAAGGCTCAATTGGGAGGTCAACGATTTGGAGAAA
TGGAAGTTTGGGCTCTGGAAGCTTATGGGGCTTCTTATACTTTACAAGAAATTTTAACAGTAAAATCTGATGATGTTGCTGGTAGAGTTAAAGTTTA
TGAAACAATAGTAAAAGGTGAAGAGAATTTCGAGTCAGGAATACCTGAGTCATTTAATGTTTTAGTAAAAGAAATCAAAGCGCTAGCTCTTAATGTG
GAGTTAAATTAAAATGAAAAAAGATATTAAAGATTTTTTTAAAGAAACTGCCATATCAGACTCTCAAAATTTTAATAGTATTAAAATTACTTTAGCA
AGCCCTGAAAAGATAAAGTCATGGACTTATGGAGAAATAAAAAAACCCGAAACTATTAATTATAGAACTTTCAGACCTGAAAAAGACGGCCTATTTT
GTGCGAGAATATTTGGTCCAATAAAAGATTACGAATGTTTATGTGGAAAATATAAAAGAATGAAGTTCAGAGGAATTATTTGTGAGAAGTGTGGCGT
AGAGGTTACTAAATCAAATGTTCGTAGAGAAAGAATGGGGCACATCAATTTATCAACCCCAGTTGCACATATTTGGTTTTTAAAATCTTTACCAAGT
AGAATTTCACTAGCTATTGATATGAAGCTTAAAGAGGTTGAAAGAGTTCTATACTTTGAAAGTTTTATTGTTATAGAGCCTGGATTAACTAGTCTTA
AAAAAAATCAACTTTTAAACGAAGATGAATTAAATAAATATCAAGAGGAGTTTGGTGAAGAATCCTTTACTGCAGGAATAGGAGCAGAGGCGATACT
AGAGATTTTAAAATCTATAGACTTGAATAAAGAGAGAGAAATTTTATTAAAAAATATAAATGAGACAAAATCAAAGGTTGCTGAAGAAAGATCTATA
AAAAGATTAAAACTGATCGATTCATTTATTGAAACTGGTAACAAACCAGAATGGATGATTTTAACTACTATACCTGTAATACCACCAGAGTTAAGGC
CACTTGTTCCTCTAGATGGAGGTAGATTTGCAACATCAGATCTAAACGATTTGTATAGAAGAGTTATAAATAGAAATAATAGATTGAAAAGATTAAT
GGATCTTAAAGCTCCAGATATAATTATTAGAAATGAAAAACGAATGTTGCAAGAGTCAGTGGATGCTTTATTCGATAATGGCAGAAGAGGCAGAGTA
ATTACAGGAACTGGTAAACGTCCATTAAAATCTTTGGCTGAAATGCTTAAAGGAaaacaaG

partial.tbl

>Feature Cont3
<1   >497 gene
            locus_tag KCS_111011
<1   497 CDS
            note    similar to Bacillus subtilis aldolase
            product aldolase-like protein
            codon_start     3
            protein_id  gnl|dbname|KCS_111011
            transcript_id   gnl|dbname|mrna.KCS_111011
<1   >497 mRNA
            product aldolase-like protein
            protein_id  gnl|dbname|KCS_111011
            transcript_id   gnl|dbname|mrna.KCS_111011
<499 >1516    gene
            locus_tag KCS_111012
499 >1516    CDS
            product actin-like protein
            protein_id  gnl|dbname|KCS_111012
            transcript_id   gnl|dbname|mrna.KCS_111012
<499 >1516    mRNA
            product actin-like protein
            protein_id  gnl|dbname|KCS_111012
            transcript_id   gnl|dbname|mrna.KCS_111012

Features on the complementary strand

Both genes are on the minus strand. The first CDS begins at nt1018 and is 3' partial. The second CDS is partial at its 5' end, at the end of the sequence at nt1516, and ends at nt1020. The first complete codon begins at nt1514, so it has codon_start=3.

complementary.fsa

>AMCont1022  [organism=Burkholderia terrae DEF2] [strain=DEF2] [isolation-source=soil in forest] [geo_loc_name=USA: Maryland]
CTTGTTTTCCTTTAAGCATTTCAGCCAAAGATTTTAATGGACGTTTACCAGTTCCTGTAATTACTCTGCC
TCTTCTGCCATTATCGAATAAAGCATCCACTGACTCTTGCAACATTCGTTTTTCATTTCTAATAATTATA
TCTGGAGCTTTAAGATCCATTAATCTTTTCAATCTATTATTTCTATTTATAACTCTTCTATACAAATCGT
TTAGATCTGATGTTGCAAATCTACCTCCATCTAGAGGAACAAGTGGCCTTAACTCTGGTGGTATTACAGG
TATAGTAGTTAAAATCATCCATTCTGGTTTGTTACCAGTTTCAATAAATGAATCGATCAGTTTTAATCTT
TTTATAGATCTTTCTTCAGCAACCTTTGATTTTGTCTCATTTATATTTTTTAATAAAATTTCTCTCTCTT
TATTCAAGTCTATAGATTTTAAAATCTCTAGTATCGCCTCTGCTCCTATTCCTGCAGTAAAGGATTCTTC
ACCAAACTCCTCTTGATATTTATTTAATTCATCTTCGTTTAAAAGTTGATTTTTTTTAAGACTAGTTAAT
CCAGGCTCTATAACAATAAAACTTTCAAAGTATAGAACTCTTTCAACCTCTTTAAGCTTCATATCAATAG
CTAGTGAAATTCTACTTGGTAAAGATTTTAAAAACCAAATATGTGCAACTGGGGTTGATAAATTGATGTG
CCCCATTCTTTCTCTACGAACATTTGATTTAGTAACCTCTACGCCACACTTCTCACAAATAATTCCTCTG
AACTTCATTCTTTTATATTTTCCACATAAACATTCGTAATCTTTTATTGGACCAAATATTCTCGCACAAA
ATAGGCCGTCTTTTTCAGGTCTGAAAGTTCTATAATTAATAGTTTCGGGTTTTTTTATTTCTCCATAAGT
CCATGACTTTATCTTTTCAGGGCTTGCTAAAGTAATTTTAATACTATTAAAATTTTGAGAGTCTGATATG
GCAGTTTCTTTAAAAAAATCTTTAATATCTTTTTTCATTTTAATTTAACTCCACATTAAGAGCTAGCGCT
TTGATTTCTTTTACTAAAACATTAAATGACTCAGGTATTCCTGACTCGAAATTCTCTTCACCTTTTACTA
TTGTTTCATAAACTTTAACTCTACCAGCAACATCATCAGATTTTACTGTTAAAATTTCTTGTAAAGTATA
AGAAGCCCCATAAGCTTCCAGAGCCCAAACTTCCATTTCTCCAAATCGTTGACCTCCCAATTGAGCCTTA
CCACCAAGAGGTTGTTGTGTAACTAAACTATAAGGACCTGTAGATCTTGCGTGTATTTTATCTTCTACAA
GATGGTGTAATTTTAACATATAAATAGTGCCAACTGTGACTTCTCTATCAAATTTTTCACCTGTTCTACC
ATCCCACAATTTTGTTTGACCAGATTTTGGTAATGATGCAAGCTCTAACATATTTGTTACATCTTGCTCT
TTTGCGCCATCAAAAACTGGTGTTGAAATTGGAATTCCACTTTGCA


complementary.tbl

>Feature AMCont1022
1018    >1   gene
            locus_tag   AMt_11123
1018    >1   CDS
            product hypothetical protein
            protein_id  gnl|dbname|AMt_11123
<1516    1020    gene
            locus_tag   AMt_11124
<1516    1020    CDS
            product oxidase
            codon_start 3
            protein_id  gnl|dbname|AMt_11124