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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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Efficient substring matching in perl

I am looking for an efficient solution to do find the longest possible substring in a string tolerating n mismatches in the main string Eg: Main…
Abhi
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multiFASTA file processing

I was curious to know if there is any bioinformatics tool out there able to process a multiFASTA file giving me infos like number of sequences, length, nucleotide/aminoacid content, etc. and maybe automatically draw descriptive plots. Also an R…
Federico Giorgi
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Error installing XML::DOM::XPath

I've written a small Perl script that uses the Bio::Seq and Bio::SeqIO packages. When I try to run the script on a linux-based server. I got a lot of errors which basically told me that BioPerl hadn't been installed. I installed ActiveState Perl…
Nottuh
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Installing Bio::DB::Sam perl module

I am trying to install a perl module Bio::DB::Sam on my home directory on a remote server. I downloaded the module, extracted the files, and ran: perl Build.pl prefix=~/local this is what happens next: This module requires samtools 0.1.10 or higher…
Nikleotide
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Issues installing perl module Bio::Perl

I am having some issues installing Bio-DB-HTS (https://github.com/Ensembl/Bio-DB-HTS) requried to run a perl script from a cloned git repository. System & Perl information I am on Mac OSx High Sierra v.10.13.6 and using perl 5, version 18,…
S.Jamal
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How do I get gene features in FASTA nucleotide format from NCBI using Perl?

I am able to download a FASTA file manually that looks like: >lcl|CR543861.1_gene_1... ATGCTTTGGACA... >lcl|CR543861.1_gene_2... GTGCGACTAAAA... by clicking "Send to" and selecting "Gene Features", FASTA Nucleotide is the only option (which is fine…
user2509933
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how to Run 'Build installdeps' to install missing prerequisites

Trying to run a Build.PL file and get following, and not uncommon error message: Checking prerequisites... build_requires: ! Test::Most is not installed recommends: * HTML::TableExtract is not installed * Math::Random is not…
brucezepplin
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Bioperl: notes or online references for beginners

Please suggestion, I want to get started from 0. I do have experience on R.
John Clark
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Editing help with perl script to start and stop at specific places within an array

Looking for troubleshooting and editing help. This is a homework assignment. My professor encourages the use of forums. I don't have experience with Perl Functions or Subs yet so please limit responses to the appropriate level so I can…
Koala
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How to get all feature in a range from a GFF3 file in Perl?

I would like to write a Perl function that gets a GFF3 filename and a range (i.e. 100000 .. 2000000). and returns a reference to an array containing all names/accessions of genes found in this range. I guess using bioperl will make sense, but I have…
David B
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Using Bioperl to alter nucleotides at specific positions in fasta file?

I am trying to adapt a Bioperl script to change nucleotides at specific positions in a fasta file and output a new file with altered sequences. Example of fasta input: >seq1 AAATAAA Example of nucleotide postions to change…
Amy Ellison
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Is there a Bioperl equivalent of IO::ScalarArray for array of Seq objects?

In Perl, we have IO::ScalarArray for treating the elements of an array like the lines of a file. In BioPerl, we have Bio::SeqIO, which can produce a filehandle that reads and writes Bio::Seq objects instead of strings representing lines of text. I…
Ryan C. Thompson
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Calculating the distance between atomic coordinates

I have a text file as shown below ATOM 920 CA GLN A 203 39.292 -13.354 17.416 1.00 55.76 C ATOM 929 CA HIS A 204 38.546 -15.963 14.792 1.00 29.53 C ATOM 939 CA ASN A 205 39.443 -17.018 11.206 …
user1866262
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BioPerl & CPAN - Problems in installation & error "Can't locate Bio/EnsEMBL/Registry.pm in @INC"

I'm posting this message out of pure desperation, because I really don't know what else to try. I'm a beginner in bioperl and I'm working on a script to parse out some results I got from MolQuest fgenesh. Results are out in .txt format and I want to…
user1192137
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Convert GenBank Flatfiles to FASTA

I need to parse a preliminary GenBank Flatfile. The sequence hasn't been published yet, so I can't look it up by accession and download a FASTA file. I'm new to Bioinformatics, so could someone show me where I could find a BioPerl or BioPython…
user81997
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