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-boun...@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] > _______________________________________________ > EMBOSS mailing list > EMBOSS@lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss