Hi Charles, I wasn't sure you'd already got a reply to this so here goes. From a very quick look at your email ... does it all make sense considering that needle does an optimal alignment with gaps whereas vectorstip uses a "word-match" type (ungapped) alignment ... ?
It seems OTT to make vectorstrip do a optimal alignment but I guess its possible in principle ... If you've still got a prob. feel free to get back. Cheers Jon > Dear list, > > I am using vectorstrip to find PCR primers in cloned PCR products. Strangely, > in some cases it misses a primer, because it overestimates the number of > mismatches. > > In the following example, vectorstrip identifies the first primer with six > mismatches, although it has only two. It means that if I run vectorstrip with > a -mismatch value lower that 29, I do miss the primer. > > The following is a mixture of shell commands and extracts of outputs. The > sequence consists of two reads assembled by using trimseq on .ab1 files, and > then merger on the resulting fasta files. > > > export > SEQ="ttttcccccccccnntttttttnnnnncccccnnnnnnnnnaaaaAAccCcTcNCTaTagggCGAGTTggGccCtTCTAGTNtGCATGCtTCGAGcGGcccGccAGTgTTGATGGaTaTCTTGCaGaaTTcGcccTTaaTGAggTAACCgGTTcccAGCaGNttttttttttttttttttttttttttttttttttttttttttttttttttttttttttAaaaaGaaTTGtttattTACTGAACCNgggCAtAtTaGaTACACAACCCATTTTaaaTTTAcATcttttAAtTCaaTtTTGAAgTGttTTTAcAcAcCCNCNCAAaAaaaaaaaaaTTTGGCATGcAACAgCTgGGAACCGTtACCtCATTAAgggCGAAtTCcAGcAcAcTGGCgGCCGTTACtAAGGGATCCGAGCTcGGNACCAAGnnnngnnnnnnnnnnnnnnnnnnttntttnntnnnnaaaaa" > > export LINKERA="AATGAGGTAACGGTTCCCAGC" > > export LINKERB="GCTGGGAACCGTTACCTCATT" > > vectorstrip asis:$SEQ \ > -linkera=$LINKERA \ > -linkerb=$LINKERB \ > -outfile stdout \ > -outseq /dev/null \ > -novectorfile \ > -nobesthits \ > -mismatch 30 > > > Sequence: asis Vector: no_name > 5' sequence matches: > From 138 to 158 with 6 mismatches > 3' sequence matches: > From 351 to 371 with 0 mismatches > Sequences output to file: > from 159 to 350 > CaGNtttttttttttttttttttttttttttttttttttttttttttttt > ttttttttttttAaaaaGaaTTGtttattTACTGAACCNgggCAtAtTaG > aTACACAACCCATTTTaaaTTTAcATcttttAAtTCaaTtTTGAAgTGtt > TTTAcAcAcCCNCNCAAaAaaaaaaaaaTTTGGCATGcAACA > sequence trimmed from 5' end: > ttttcccccccccnntttttttnnnnncccccnnnnnnnnnaaaaAAccC > cTcNCTaTagggCGAGTTggGccCtTCTAGTNtGCATGCtTCGAGcGGcc > cGccAGTgTTGATGGaTaTCTTGCaGaaTTcGcccTTaaTGAggTAACCg > GTTcccAG > sequence trimmed from 3' end: > gCTgGGAACCGTtACCtCATTAAgggCGAAtTCcAGcAcAcTGGCgGCCG > TTACtAAGGGATCCGAGCTcGGNACCAAGnnnngnnnnnnnnnnnnnnnn > nnttntttnntnnnnaaaaa > > needle asis:$SEQ[138:158] asis:$LINKERA stdout -auto > > asis 138 aaTGAggTAACCgGTTcccAG- 158 > |||||||||| |||||||||| > asis 1 AATGAGGTAA-CGGTTCCCAGC 21 > > > Interestingly, in the following aligmnent, the number of mismatches is > 6. But I did not find anything saying that gaps were disallowed in > vectorscript ? > > aaTGAggTAACCgGTTcccAG > ||||||||||| | | || > AATGAGGTAACGGTTCCCAGC > > > I am using emboss through fink (emboss package 4.0.0-2). > > Have a nice day, > > -- > Charles Plessy > http://charles.plessy.org > Wako, Saitama, Japan > _______________________________________________ > EMBOSS mailing list > [email protected] > http://lists.open-bio.org/mailman/listinfo/emboss > _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
