This is a test version of Biostars. For the public version, visit https://www.biostars.org.
CAP3 result interpretation

I am working on analysis of ESTs for cotton, extracted from dbEST, NCBI. For assembly I subjected non-redundant sequences to CAP3 assembly server (from Citrus genome database). I got following files.

  1. (filename).fas.1.txt.IN.cap.contigs
  2. (filename).fas.1.txt.IN.cap.singlets
  3. (filename).fas.1.txt.IN.cap.contigs.singlets.txt
  4. (filename).fas.1.txt.IN.cap.summary.txt
  5. (filename).fas.1.txt.IN.txt
  6. (filename).fas.1.txt.OUT.txt

Among these files, the top three files contain just sequences as contigs and singlets. The last file contains annotation numbers etc. of these contigs and singlets. But for further analysis such as BLAST(through Blast2GO) I need sequences in FASTA form. How can I convert these sequences into FASTA form.

est cap3
• 3,462 views • link
updated by Ram Ram • written by meghasihag • meghasihag

The (filename).fas.1.txt.IN.cap.contigs and (filename).fas.1.txt.IN.cap.singlets should be in FASTA format already. Did you try to see their contents?

• 0 views • link
updated by Ram Ram • written by GouthamAtla GouthamAtla

Yeah, but only (filename).fas.1.txt.IN.cap.singlets is in FASTA format.

and (filename).fas.1.txt.IN.cap.contigs is like this

>Contig1
NAAAAGTATAGGCTCGAGAGAGAAGTCCTGGCCTATCGGATTACACCACGNGTCAGATCT
GTCACTTCAAGGAGCTTTTCAGCGTCTTTGACAAGAATGGCNGACGGTTGCCGTCCTTCC
AGGGAGATTGGGGCAGAATTCGAGTCACTGCCNGTGGATTCCTTAGTGATCCAGATGTCG
GATATATGTCCAATATAGCCAATNGTTGTTGGACATAGCACCATCAATCATCAAGATTGC
TATTTCGCCACCTCNATGTAGAGTGGAAGATCCAAATGCGGGAATGGATTTCAAGGTTGG
TTAAGNATGGGGGCAGCGGATGAGTTAACAGTACAGCAAGCTAGGCAGCTCCATTTNTGA
CTTGGAATCTTCATACGATTCATTTATGGCAGCTTTGCCTAATGTTGNGTACTTGAAAGT
AAAATCCAATATTTCCATATTTTTGTTTAGTGCTTCAAATCTGGTGAGAACGGATGTTTT
AAGTTGGTAAAACAGTGTATTCATTTTGAAGAGTTCTTGGATTGTTTAAAGCTCAAGATG
CTATTTGTGTGCTGCTGATTTGTCGTTCTATGAGAAAGAATATATGCTTTAATTTGGTTT
TGTAATATTAANTATATTCATTCCCCTTGATTGTTGTTTTGTNNNNNNNNNNNNNNNNNN
NN
>Contig2
NTGTTTTTTCTTTACTCGGTGTCTCGTCGGTACTCGACGACTAAANGGGNTATAGGAGGG
GCGCGAACGNCGAAACGGGAGTGGGTACAAAGCGTGGTCCNGGATAGACGAGAGCGGACG
CGCCGGGTGAAGCTCGGCGCGACGCGAGGCANAGAGGGGCCCGCAGANNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNAAGNCCCAGGATGCGCATCGCCCCAGGGGTGAAACCCCCATCCCAAAGAA
TGCTNCTCCTNCGCGGTAGGGCAGCTNCCCGAAGCACCCGACCGCTTTNAGGCCANCCAT
ATGATAAAGNAACGTTGTGTGGTGAATGGGATGAAGATGATTGAAGNAGAGTAGAGTTTT
GCCTCTANATCTTGATATGTATATCTTTAATTATATAANTATAGCTCATTATATTGTGCN
TTAGCATGTAATATTTAAGTCTAAAATTAANTGGACCTCAGCTCGAGGTCGNCATTCTTT
GTTACTTTAGATCAGATCTGTANTTCCCTTTGTATTGTTCAGGNTTTCCAACCATAAATT
ATTGGTACTATCTTNATTGTTATCATAATTGACGTGTGTTTAAGTTCNNNNNNNNNNNNN
NNNNN
• 0 views • link
updated by Ram Ram • written by meghasihag • meghasihag

0 answers

No answers yet.

Log in to answer this question.

More posts like this