Hello all,
I have obtained HMMER reads on 60 metatranscriptomic sequences, against Pfam, dbCAN2, and MEROPS databases. I ran the protein...
26 results in 0.0023 seconds.
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Parsing HMMER Reads in Biopython
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Parsing Blast xml using Perl (BioPerl)
Hi people,
I'd like to resolve the following problem(s):
I'm trying to resolve the structure of reads, partial of retroviral origin,... -
Blast HSP tiling BioPerl Module Query
Hi,
Greetings!
I have one query regarding HSP tiling. I want to parse tblastn output to merge all overlapping HSPs and also... -
using bioperl to parse genome based on basepair location
Hello all
I have a genome that I am looking to parse a genome based on another file that has a name associated with the coordinates of the specific...Last edited by ninja_help; 08-06-2015, 02:15 PM. -
Extract sequences from fasta in Windows
Hello everyone,
I'm a very beginner at bioinformatics and I got a terrible score in a programming exam while I was an undergrad...
... -
Bio-SamTools pileup method
Hello
Im trying to use Bio:: DB::Sam to get list of reads covering certain position .Sam file using pileup method using this code
...Code:use strict;
Last edited by m4merg; 07-31-2014, 08:19 AM. -
How to implement Clustalw in Perl Program
Please be kind to suggest how to implement clustalw in a perl program.
What all steps I need to follow.
Also , I have referred to... -
Bioperl error in bacterial annotation
Hi, I installed PROKKA pipeline for annotation of a bacterial genome. One of its dependencies is BioPerl, I installed this according to http://www.bi... -
sort contigs based on fasta header
Hello All,
I have a problem that I am looking for some input on.
I have been using the genome assembler SPAdes, which... -
Stuck at blast in Bio perl
Hi All,
I am newbie in bio perl.
I want to blast a sequence using, standAloneBlast and parse its output later.
I have my blast+... -
unable to use Bio::Seq in perl
Hi Forum Members,
OS: Ubuntu 12.04
Perl: 5.14
I am facing issues working on Bio:
erl
Steps I followed:
1) CPAN... -
Parsing a GenBank file
Hi,
I would be happy if someone could help me get the following code to output the sequences (including the ids) of all records in the... -
How to compare two hsps with each other?
Hi there! I have small problem.
Within BioPerl I use SearchIO to parse my BLAST-output. Within this, the output is a result, which contain... -
Bioperl MSG: seq doesn't validate fetch genbank from NCBI using GI
I am trying to fetch genebank features, this code works for some GenbankIDs but not for this one as an example.
use strict;
use warnings;... -
Sequence from Genbank file
Hi,
I used to usethis code to download sequence from genabnk ,now bioperl complains about sequence is empty, do yiu know if gen bank structure...
