hyphaltip

the .blast is tblastn from BLAST+ run with -max_intron_length 300 and the text or -outfmt 6 output is shown. 

the wublast output is from tblastn run with -links and hspsepsmax  - you can see the two group as an HSP group (hits 3 and 4 out of the set).

hyphaltip

Hi all, 

  Cluless newbie here (first time touching Perl 48 hours ago...), for which apologies. 

I'm trying to take a genbank file (.gb), and create a FASTA file with a specific identifier line for each sequence. Specifically, I want the "host" tag as the identifier. With the help of the Bioperl beginner readme and the HOWTO's (which are great!) I've worked out how to loop through my sequences and get the 'host' tag for each one. For some reason, I get two identifier lines for each sequence. I guess the problem is in the 'for' loop--it's running the stuff below it twice, once with the actual 'host' tag data and once with...nothing? Not sure.
I think I can work out how to use s/ and a regex just to delete the second identifier line, but that feels like I'm avoiding the problem instead of fixing it.  Any help appreciated!

Many thanks,

haywardjeremya@gmail.com

hyphaltip

#!/usr/bin/perl
use warnings;
use strict;
my $seq ="AGACAAGTCGGACGTTTCATCTGAGGGTTCTTCTGCCTCCGCACTTGGTGCACATCAGACAAGGCAATCA
TGGGGGACGCTCAGATGGCAGAGTTTGGAGCAGCAGCTTCTTACCTGCGAAAGTCAGATCGAGAGCGTCT
GGAAGCACAAACCCGTCCCTTTGATATGAAAAAGGAGTGTTTTGTGCCTGATCCAGATGAAGAGTATGTA
AAAGCTTCAATCGTCAGTCGTGAAGGTGACAAAGTCACTGTACAGACTGAGAAAAGAAAGACTGTAACTG
TAAAGGAAGCTGACATTCACCCCCAGAACCCTCCAAAGTTTGATAAAATTGAAGACATGGCAATGTTCAC
CTTCCTTCATGAGCCAGCCGTGCTGTTCAACCTCAAAGAGCGCTATGCAGCATGGATGATCTATACCTAC
TCAGGACTGTTTTGTGTCACTGTCAACCCCTACAAGTGGCTGCCGGTGTACAATCAGGAGGTGGTTGTAG

hyphaltip

#!/usr/bin/perl
use warnings;
use strict;

my $seq ="AGACAAGTCGGACGTTTCATCTGAGGGTTCTTCTGCCTCCGCACTTGGTGCACATCAGACAAGGCAATCA
TGGGGGACGCTCAGATGGCAGAGTTTGGAGCAGCAGCTTCTTACCTGCGAAAGTCAGATCGAGAGCGTCT
GGAAGCACAAACCCGTCCCTTTGATATGAAAAAGGAGTGTTTTGTGCCTGATCCAGATGAAGAGTATGTA
AAAGCTTCAATCGTCAGTCGTGAAGGTGACAAAGTCACTGTACAGACTGAGAAAAGAAAGACTGTAACTG
TAAAGGAAGCTGACATTCACCCCCAGAACCCTCCAAAGTTTGATAAAATTGAAGACATGGCAATGTTCAC
CTTCCTTCATGAGCCAGCCGTGCTGTTCAACCTCAAAGAGCGCTATGCAGCATGGATGATCTATACCTAC

hyphaltip

#!/usr/bin/perl -w
use strict;
use warnings;

use Bio::SeqIO;
use Bio::Seq;
use Bio::AlignIO;

my $sequence;
my $seq_obj;

hyphaltip

#!/usr/bin/perl
use strict;
use warnings;

my @seqnames = ("AAC35278", "AnCSMA", "AfCHSF", "AAF19257", "P30573-1");
my @seqs = ("LLIAITYYNEDKVLTARTLHGVMQNPAWQKIVVCLVFDGIDPVLATIGV-VMKKDVDGKE","AMCLVTCYSEGEEGIRTTLDSIALTPN-SHKSIVVICDGIIKVLRMMRD-TGSKRHNMAK", "ALCLVTCYSEGEEGIRTTLDSIAMTPN$

for ( my $i = 0; $i <= 4 ; $i++) {
print "Sequence name is $seqnames[$i]\n";
my @residues = split('-',$seqs[$i]);

hyphaltip

#!/bin/perl -w
#sort sequences into two files according to 5' barcode

use strict;
use warnings;
use Bio::SeqIO;


my $file = 'trimmed_seq.fa';
my $in = Bio::SeqIO->new(-format => 'Fasta',

hyphaltip

hyphaltip

#module load emboss (need emboss tools - install on mac with homebrew or other methods)
#download
curl -C - -O  http://microsporidiadb.org/common/downloads/Current_Release/NparisiiERTm1/fasta/data/MicrosporidiaDB-26_NparisiiERTm1_AnnotatedCDSs.fasta
curl -C - -O http://microsporidiadb.org/common/downloads/Current_Release/NematocidaSp1ERTm2/fasta/data/MicrosporidiaDB-26_NematocidaSp1ERTm2_AnnotatedCDSs.fasta
curl -C - -O http://microsporidiadb.org/common/downloads/Current_Release/NparisiiERTm3/fasta/data/MicrosporidiaDB-26_NparisiiERTm3_AnnotatedCDSs.fasta

geecee MicrosporidiaDB-26_NematocidaSp1ERTm2_AnnotatedCDSs.fasta Nsp1ERT2.geecee
geecee MicrosporidiaDB-26_NparisiiERTm1_AnnotatedCDSs.fasta NparERT1.geecee
geecee MicrosporidiaDB-26_NparisiiERTm3_AnnotatedCDSs.fasta NparERT3.geecee

hyphaltip

CLUSTAL FORMAT for T-COFFEE Version_8.97_101117 [http://www.tcoffee.org] [MODE:  ], CPU=0.01 sec, SCORE=88, Nseq=4, Len=381

NCU05969          MPSFTSKSLLAVLAGAASVAAHGHVSNIVINGEYYRGFDS-SLNYMANPP
NCU07898          MKTF-----ATLLASIGLVAAHGFVDNATIGGQFYQPYQ---DPYMGSPP
NCU07760          MARM---SILTALAGASLVAAHGHVSKVIVNGVEYQNYDPTSFPYNSNPP
TRIREDRAFT_73643  MIQKLSNLLVTALAVATGVVGHGHINDIVINGVWYQAYDPTTFPYESNPP
                  *         : **    *..**.:..  :.*  *: ::     * ..**

NCU05969          AVVGWKANNQDNGFVGPDAFSSPDIICHKDATNAKGHAVVKAGDKISIQW
NCU07898          DRISRKIP--GNGPV--EDVTSLAIQCNADSAPAKLHASAAAGSTVTLRW