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Questions tagged [bioperl]

BioPerl is a package of Perl tools for computational molecular biology.

BioPerl is a toolkit of Perl modules useful in building bioinformatics solutions in Perl. Addition auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as Git modules in their repository.

References:

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BioPerl with clustalw - outputting file

I have a perl script to automate many multiple alignments (I'm making the script first with only one file and one multiple alignment - big one though. I can then modify for multiple files) and I want to output the resulting file, but I am unsure on…
SJWard
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How can I download the entire GenBank file with just an accession number?

I've got an array full of accession numbers, and I'm wondering if there's a way to automatically save genbank files using BioPerl. I know you can grab sequence information, but I want the entire GenBank record. #!/usr/bin/env perl use strict; use…
Steve
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search sequence in genome with mismatches

i have a fastq file with more than 100 million reads in it and a genome sequence of 10000 in length i want to take out the sequences from the fastq file and search in the genome sequence with allowing 3 mismatches I tried in this way using awk i got…
abh
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BioPerl module Bio::DB::EntrezGene no longer working

I've been using the Bio::DB::EntrezGene module from BioPerl to retrieve Entrez gene names given the numerical ID. This worked fine for months, and as recently as two weeks ago. Recently, though, it only returns an error. The strangest thing (to me)…
Matt LaFave
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Perl how to catch two exceptions thrown at once

I am parsing a large EMBL file (>1G) and convert it to a gff file. It has some entries are not matching the traditional embl formation thus cause the bioperl module to throw exceptions. My question is since entries with error are only small…
user2241994
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Export sequences to fasta wide format

I'm trying to export aligned sequences to a fasta file one by one using Bio::SeqIO. The result is that the sequences are broken by a new line every 60 columns. How do I avoid that? I'd like to have the sequences exported in a 'wide' format, i.e. no…
Roey Angel
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alignment of sequences

I want to do pairwise alignment with uniprot and pdb sequences. I have an input file containing uniprot and pdb IDs like this. pdb id uniprot id 1dbh Q07889 1e43 P00692 1f1s Q53591 first, I need to read each line in an input file 2)…
user2053919
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Installing Bio::Restriction::Analysis in Strawberry Perl

I am attempting to install the module Bio::Restriction::Analysis in Strawberry Perl (v5.16.1.1 32 bit) using CPAN. However, it looks like it won't pass a few tests. Portions of CPAN's output are below. Running Build test t/Align/AlignStats.t…
indiguy
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Bioperl reading fasta sequences

I found that if my fasta file ends with a single line sequence then that sequence returned by Bioperl will have one nucleotide missing. If fasta file ends with the new line then it returns complete sequence. Don't understand why? Is this a…
Andriusa
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Perl: Finding _ followed by X with stuff in between

many thanks for the help with the earlier issues. I've almost finished the last thing I was working on - specifically an ORF (open reading frame) finder program. So far, I've got an array called @AminoAcidArray1. All the start codons are "_" and…
Shtanto
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how to run local blast program in apche2 server

I am running a local blast program in apche2 server...but it showing me error that. --------------------- WARNING --------------------- MSG: cannot find path to blastall My code is.. #!/usr/bin/perl print "Content-type: text/html\n\n"; use…
Manju
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Scripts_for_GB error: number of input seqs differ (aa: 0; nuc: 2)!! and Possible precedence issue with control flow operato

I am trying to calculate ka and ks, so I am using the test data available here: https://github.com/qiao-xin/Scripts_for_GB Howerver,I have an error: perl calculate_Ka_Ks_pipe.pl -d data/Ath.cds -g data/Ath.tandem.pairs -o result/Ath.td.kaks Possible…
Dayana Turquetti
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How to solve segmentation fault (core dumped) while reading SCF files?

I got segmentation fault (core dumped) error when I try read SCF file. I'm using Bio::SCF module in perl and just followed the example from "https://metacpan.org/pod/Bio::SCF". The code is as below ... #!/usr/bin/perl use warnings; use…
Yushin Jung
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How to match two .csv files and write on third file replacing data in file 2 with data from file 1

I have 2 csv and text files, file 1 has 2 columns one with gene id and two with gene name,file 2 has many columns with part of the string in columns being gene id e.g gene id(genome) or pseudo gene id(genome). i want to compare each gene id in file…
Mutua Mwikali
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sorting a multiFASTA file by DNA length

I'm trying to sort a multiFASTA file by length. I have the alphabetical sort figured out but I can't seem to get the numerical sort. The output should be a sorted multiFASTA file. This is an option to another program. Here is the code. sub sort { my…
Jeffery Rosario
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