BioPerl

Hi Mark, Does you GFF have a line that identifies the reference sequence, like this: SEQ1 . contig 1 123456 . . . Name=SEQ1 If not, that could be the problem. Scott On Wed, May 14, 2014 at 5:22 AM, Mark Wilkinson <markw< at >illuminae.com> wrote:

Hi! I'm using BioPerl to work with GenBAnk files, mostly public files from the NCBI. For GenBank files with a CONTIG line like thw following "CONTIG join(BA000030.3:1..9025608)" the Genbank parser does not work properly. As a simple example: ... [More] *#!/usr/bin/env perluse strict;use warnings;use Bio::SeqIO;my $file = shift;# create reader for the inputmy $seq_in = Bio::SeqIO->new( -file => $file, -format => 'genbank' );my < at >entries;while (my $contig = $seq_in->next_seq()){ ## do stuff push < at >entries, $contig;}my $outfile = Bio::SeqIO->new( -file => ">out.gbk", -format => 'genbank' );foreach my $contig (< at >entries){ $outfile->write_seq($contig);}* This script creates a Genbank file, but the genome sequence is missing. This is independent from what I do in the "do stuff" part, even this empty version does not export a sequence. The problem seem [Less]

Hi all BioPerlers! I'm confused by something. In the scenario below I have a Fasta file and a GFF file: ========= File: a.fas >SEQ1 AAAATTTTCCCCGGGG ========= File: b.gff SEQ1 hit1 match_part 1 5 . . . . SEQ1 ... [More] hit2 match_part 6 10 . . . . ========= I load them into a seqfeature DB: bp_seqfeature_load.pl -d dbi:mysql:seqdb -c -u root -p pass a.fas b.gff I then explore the data as follows: use Bio::DB::SeqFeature::Store; my $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql', -dsn => 'dbi:mysql:seqdb', -user => 'root', -password => 'pass'); my $iterator = $db->get_seq_stream(); while (my $feature = $iterator->next_seq){ print $feature->seq->seq; # THE SEQUENCE IS PRINTED print " comes from sequence named "; print $feature->seq->id; # THE METHOD ABOVE RETURNS UNDEF } my $seq = $db->segment('SEQ1'); # $seq is undef, NOTHING IS RETURNED!?!? ============ This is all very confusing. [Less]

I'm getting this error message when trying to do the beginners how-to: Replacement list is longer than search list at C:/Perl 164/site/lib/Bio/Range.pm line 251 The example scripts seem to run normally but I was wondering if there was a way to prevent this warning... -Charlie

Hi, I have a script that runs blast jobs against the databases at the NCBI. I use the Bio::Tools::Run::RemoteBlast module for the blasting. It was working but is not now. The following is an example of the response I now get: ... [More] --------------------- WARNING --------------------- MSG: req was POST http://www.ncbi.nlm.nih.gov/blast/Blast.cgi User-Agent: bioperl-Bio_Tools_Run_RemoteBlast/1.006901 Content-Length: 788 Content-Type: application/x-www-form-urlencoded DATABASE=nr&QUERY=%3EHCV-54_contig_15+%0D%0ATCATAACAACCTTTTATGGTAAATACTAACAGCATGCCCATTTTACATGTGAGGAAACTGAGGCTTAGATCAGGTAAGTAGCTTATTCAGTGTTGCTCAAGTAAATACGTTTTAAGAACCCTCAGCCTCGCTCTCCTCTTCCTCAGGGCACACTTTTTTTTTTTTCCTTCCTACTGTGTGAGCTGTGGTGGGAATGTTAATCGGGATGCCTGTCTTTCCCTAGTCTTGGGGTCAGGCAAGTGCTCAAAGTCAGGATAAGCAAACTCTCCTTCCTGGGACTCTGAGGAAAGGCTCATTGATGGGGGAAATGGAGGGAGTGGATTCACTCCAGCTCAGCTCCGGGACAAGATGGCCATGGAGCTCCTGCTACATAAATGTCAGGGACTATCCTGGCTCCATCCTGCCTGCTTCCCTAGCTGCTGCCCAGCACTCACCTTATAAACATCCTTCGAGCTGGAGTTAGCCCGAATTGGTTTCTGTCCCTTGTGACCACTGAGCCCTGGCTGACA [Less]

Or ggsearch or ssearch in fasta package Jason Stajich jason.stajich< at >gmail.com On Mon, May 5, 2014 at 5:58 AM, Paul Cantalupo <pcantalupo< at >gmail.com> wrote:

Hi guys, Thank you all for your replies. I'm slowly starting to understand how things work.. Christipher - I'm actually working on few different tasks - 1. Alignment of list of genes against another list of genes (blast worked well here). 2. ... [More] Alignement of genes on refference genome - here also blast did well in most cases. 3. Alignement of contigs/scaffolds on refference genome - here blast did ok for medium-size (few hundreds) sequences, but for very-long and short ones it worked so-so (found many small pieces/didn't find anything for the long/short seqs, respectively)... So, maybe I should ask - what is the best tool to re-assemble contigs/scaffolds on refference genome? Russel and Paul - from you and understand that I can use megablast or needle - are these commands implemented in perl? I want to align many sequences, so I don't want to do it manually.. Thank you, Oz On Wed, Apr 30, 2014 at 10:38 PM, Smithies, Russell [via BioPerl] < ml-node+s996286n17494h17< at >n3.nabble.com> wrote: -- View this m [Less]

Hi Oz, SInce BLAST is a local alignment tool, perhaps you want something like Needle http://www.ebi.ac.uk/Tools/psa/emboss_needle/nucleotide.html which performs a global alignment? You can add the '-perc_identity' option to the blastn command line ... [More] like so: blastn -perc_identity 80 to limit results to >=80% identity. Paul Paul Cantalupo University of Pittsburgh On Tue, Apr 29, 2014 at 12:49 PM, Oz <oz.sharabi< at >mail.huji.ac.il> wrote: [Less]

Hello bioperl support manager i have difficulty using this module actually i don't know which argument use for result method to see the result of prediction thank you _______________________________________________ Bioperl-l mailing list Bioperl-l< at >lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l

Hi Forum members, My purpose is to do multiple sequence alignment using perl script and Bioperl mdules. For that I installed Bioperl and Clusalw2 (2.1) in my Windows 7. When i tried to run a small code (attached below), it is showing some error ... [More] as "align is not recognized as internal or external command etc etc.. A screen shot is attached. I saw someone post similar error, but could not find any solution. So, kindly suggest me the solution. An Lee, Seoul, ROK Code, #!/usr/bin/perl use Bio::Seq; use Bio::Tools::Run::Alignment::Clustalw; use Bio::AlignIO; BEGIN { $ENV{CLUSTALDIR} = 'C:/ClustalW2/clustalw2.exe'} $factory = Bio::Tools::Run::Alignment::Clustalw->new(-matrix => 'BLOSUM'); $ktuple = 3; $factory->ktuple($ktuple); # change the parameter before executing $in="1.fasta"; $aln = $factory->align($in); _______________________________________________ Bioperl-l mailing list Bioperl-l< at >lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l [Less]