[EMBOSS] Antwort: vectorstrip not finding match

[david.bauer at bayer.com]

Hi Alan,

the vectorsfile for vectorstrip is not the vector sequence in fasta format 

but a file containing the 5' and 3' end sequences of the vector site, 
where the insert was cloned in.
So for the pCR4-TOPO you need this in your vectorsfile:

pCR4-TOPO       agtcctgcaggtttaaacgaattcgccctt 
aagggcgaattcgcggccgctaaattcaat

With this vectorsfile the program finds the vector in your sequence file:

> vectorstrip -seq l3.fa -vectorsfile emboss_vectors.txt


Sequence: L3-cDNA-500-PFU-clA-M13R.ab1   Vector: pCR4-TOPO
5' sequence matches:
        From 30 to 59 with 0 mismatches
3' sequence matches:
        From 540 to 569 with 0 mismatches
Sequences output to file:
        from 60 to 539
                TTAAAGAGGATCAGGTATTTTCTCCACGTGGTGCACGCAAAGCGAGTTGG
                TCGAGTGTAATTATTTCACCACCTGCTTTAATTATCCGTGCGCGAGCTCC
                TTTAGTCACATGCAGTGCAGCAACCGTAAGCTTGGGAATTTCAAAAATCC
                GATTATCATCTGTGATCGTCCCAACTACGACCGCTATTTTCGTTATATTA
                CCACCTCTTTTCATGTAACGTACCAAACGAGCAAGTGACATCGGTGGACG
                ATGGCGACGAGCCATCATTAATCTTTTCGTGATAATATTGTTGAATTTTT
                CACCGGTTTTCCGAGTCAAGTATTTGTATAACTTTACTAGGACTCGAAGA
                TACGGATCTTCACTTTTTGGTGCTTTACGCCGTACTTTACGGTCATTTTT
                ATGATTTATATCGATACCCATTTTTAATACTGGACTGCTCCCCCTCGCTA
                ATCCTGCACTCAAACTTGGGTAATTAAACC
        sequence trimmed from 5' end:
                GCGAACTAGATATCCTCACTAAAGGGACTAGTCCTGCAGGTTTAAACGAA
                TTCGCCCTT
        sequence trimmed from 3' end:
                AAGGGCGAATTCGCGGCCGCTAAATTCAATTCGCCCTATAGTGAGTCGTA
                TTACAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTG
                GCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGG
                CGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAG
                CCTATACGTACGGCAGTTTAAGGTTTACACCTATAAAAGAGAGAGCCGTT
                ATCGTCTGTTTGTGGATGTACAGAGTGATATTATTGACACGCCGGGGCGA
                CGGATGGTGATCCCCCTGGCCAGTGCACGTCTGCTGTCAGATAAAGTCTC
                CCGTGAACTTTACCCGGTGGTGCATATCGGGGATGAAAGCTGGCGCATGA
                TGACCACCGATATGGCCAGTGTGCCGGTCTCCGTTATCGGGGGAAGAAGT
                GGCTGATCTCAGCCACCGCGAAAATGACATCAAAAACGCCATTAAGCTGA
                TGTTCTGGGGAATATTAATGTCACGCATGAGATATCCAAAAAGGATCTTC
                CCCTAAATCCTTTTCTCGTATAAAGCCAGTCCGACAGAAAACCGGGGCTG
                ACCCCGGGATGAATGTCTCAACCCAACTGGGGGCAA


Hope this helps,
David.

emboss-bounces at lists.open-bio.org schrieb am 14/12/2010 19:33:36:
> Hello,
> 
>      I am having some trouble getting vectorstrip to match the vector
> sequences with the sequence data. I have attached the vector file and 
some
> of my test data along with this message. I don't know if it is a 
formatting
> error or not but I am out of ideas for this one. However, I haven''t 
used
> this software before so I may be missing something, but I listed the 
command
> line arguments that I changed (those that are prompted but NOT listed 
below
> were kept as the default settings). Please let me know if you have any
> suggestions, thank you!
> 
> Also, is there a way to trim quality files, too?
> 
> <CODE>
> vectorstrip -sequence L3-cDNA-500-PFU-clA-M13R.ab1.seq -vectorsfile
> pCR4TOPO.fasta
> -Show only the best hits? N
> <\CODE>
> 
> -- 
> 
> Alan Twaddle, B.S.
> MUC class of 2010
> [Anhang "L3-cDNA-500-PFU-clA-M13R.ab1.seq" gelöscht von David 
> Bauer/SGQRH/DE/BHC/BAYER] [Anhang "pCR4-TOPO.fasta" gelöscht von 
> David Bauer/SGQRH/DE/BHC/BAYER] 
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