Use this tag for questions relating to common bioinformatics tasks performed on a *nix system. Things like manipulating/converting between standard biological text formats, extracting data of interest from such formats etc.

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How to cut fasta sequence at specific numbers and generate ORFs

I have a file as shown below: CDS join(36..56,37..67) CDS 36..183 CDS 457..565 CDS join(505..519,521..596) CDS join(577..591,725.....
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Converting column data to matrix

I am trying to create a matrix of plant traits and plant species. There are 2,912,746 rows in the data and 3 columns. There are different numbers of traits for each species, and not every species has ...
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How do I reinstall the bioperl modules on Ubuntu?

I am trying to learn bioinformatics the hard way. I have no background in Linux, Ubuntu, bash, Perl, Python, etc. I'm trying to use several programs, mostly the bioperl modules, that have been ...
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How do I blastp multiple fasta files, and move the files with say 50 to 90% similarity to another folder?

So I have about 100 fasta files to blast and I need to find files with 50 to 90% similarities with the database file. Then the files are to be moved to a new folder. How do I do this?
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How to run a BBMap software .sh script in a for loop for a set of 100 .fasta files?

cd /home/user/Documents/bbmap ./bbmap.sh ref=fake.fa # indexes fasta format file sets ref filelist="fastaone.fasta, fastatwo.fasta, fastathree.fasta" for list in "$filelist" do ./bbmap.sh done Is ...
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Question: Running PSI-BLAST Against Multiple Queries

I'm new in standalone blast+ and in linux terminal. I set the bash-profile to load the PATH and BLASTDB for my blast already, but I don't know how to use psi-blast yet. The question is - Can I and How ...
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Drawing a histogram from a bash command output

I have the following output from a miRNA Predictor: Read Sequence:hsa-miR-576-3p MIMAT0004796 (22 nt) Read Sequence:gi|182396|gb|M74088.1|HUMFAPAPC Human APC gene mRNA, complete cds (8972 nt) ...