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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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Converting selected rows to column using perl script

I need a Perl script to concatenation the line.. I have more than 1000 gene name (>pmpI) and its function (polymorphic outer membrane protein) its is in separate line and i wish to join the function of the gene near to the gene name, so that it can…
Nitha
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API Installation Error on Mac

I'm having trouble installing the ensembl API. I've been using the installation guide on the website. First I had a hard time getting DBI and DBD mySQL modules, but once I used perlbrew I had no issues. However when running ping I get the error…
hmillss
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How to view the object arguments of a Perl module?

How do I view the arguments/parameters that can be passed to a new object on a Perl module? I usually go to CPAN and look at the SYNPOSIS section for examples of what I'm trying to do. But the examples and the descriptions they provide aren't always…
cooldood3490
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How to access the data stored in this object?

I'm using BioPerl module to obtain a string from a set of parameters. I followed the HOWTO:Beginners page. The module apparently returns a hash object. How do I get the actual string out of the hash object? use Bio::DB::GenBank; use…
cooldood3490
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Processing FASTQ files based on mate pair length

The following files are two mates of a paired-end fastq file, I want to separate each fastq based on their…
Tahmtan Ebrahimi
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Converting PHYLIP text file to a PNG image

Does anyone know how I can convert a phylip tree format file in text format to a PNG image programmically in perl? Tree file: ( B:6.0, ( A:5.0, C:3.0, E:4.0) :5.0, D:11.0); I have tried using the Bio::Tree::Tree module but it…
BioDeveloper
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extract gene-id + function annotation from .gff

i have a .gff file looking like this: Niben044Scf00000988 . contig 1 120868 . . . ID=Niben044Scf00000988;Name=Niben044Scf00000988 Niben044Scf00000988 maker gene 6221 8457 . - . …
Markus
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BioPerl: Annotate mismatches in an alignment

I'm reasonably new to perl and very new to BioPerl, so my apologies if this seems like a trivial question. I'm using Bio::AlignIO and Bio::SimpleAlign to generate pairwise alignments of sequences of interest to a reference sequence - in this case…
user2460253
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Capture Output to stream and store as a string variable

Although this question relates to 'BioPerl', the question, I believe, is probably more general than that. Basically I have produced a Bio::Tree::TreeI object and I am trying to convert that into a string variable. The only way I can come close to…
Rambatino
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Error in Bioperl program execution

I have installed bioperl but confused where to get it and where to run the bioperl program.Then I have tested for it and it was successful I have run a program for multiple seq. alignment. Generated an error Can't locate…
Rajkishore90
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Parsing GenBank file

Basically, a GenBank file consists on gene entries (announced by 'gene' followed by its corresponding 'CDS' entry (only one per gene) like the two I show here below. I would like to get locus_tag vs product in a tab-delimited two column file. 'gene'…
biotech
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Retrieve the coding amino-acid when there is certain pattern in a DNA sequence

I would like to retrieve the coding amino-acid when there is certain pattern in a DNA sequence. For example, the pattern could be: ATAGTA. So, when having: Input file: >sequence1 ATGGCGCATAGTAATGC >sequence2 ATGATAGTAATGCGCGC The ideal output would…
biotech
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parsing a multi-record GenBank File

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 input file (http://biopython.org/DIST/docs/tutorial/examples/ls_orchid.gbk): use Bio::SeqIO; use Bio::Seq; use…
user27976
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How can I modify the Smith-Waterman algorithm using substitution matrix to align proteins in Perl?

How can I modify the Smith-Waterman algorithm using a substitution matrix to align proteins in Perl? [citations needed]
may
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Read a protein fasta file and splitting the read string at Arginine(R) and then blastp the peptides to get the matches?

I have the following fasta file: '>gi|277456704|dbj|ID_P|Gene name…
RnD
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