Category Archives: Local Tools

Genome survey of resistance gene analogs in sugarcane: genomic features and differential expression of the innate immune system from a smut-resistant genotype

New manuscript on BMC Genomics. Link here! Background Resistance genes composing the two-layer immune system of plants are thought as important markers for breeding pathogen-resistant crops. Many have been the attempts to establish relationships between the genomic content of Resistance … Continue reading

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Making OrthoMCL easier to use

“OrthoMCL is an algorithm for grouping proteins into ortholog groups based on their sequence similarity. “ With more than 3K citations, the OrthoMCL elegantly finds orthologs, co-orthologs, and in-paralogs in protein FASTA files. If all that you need is to … Continue reading

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NJ trees for multiple FASTA files using Phangorn R package

This script intends to iterate with multiple-sequence alignment (MSA) FASTA files in a directory and create Neighbor-Joining (NJ) trees for each of those files. For this, we will use R and the package Phangorn. Phangorn is described as a package … Continue reading

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Find introns correspondent to CDS sequences using genomic sequences and annotation from PLAZA database

I was working with coding-DNA sequences (CDS) data from PLAZA and, at certain point, a co-worker needed not only the exons – which the CDS is constituted – but also the sequences of introns, which is any nucleotide sequence within … Continue reading

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Capture fasta sequences from file using a list of headers using Python

If you have a fasta file and want to capture some specific sequences based on a list of headers you could only use some short bash “grep” command. However, if the fasta file contains sequences in multiple lines this would … Continue reading

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ORF Finder for DNA sequence Fasta files using Python

Succinctly, an Open Reading Frame (ORF) is a part of DNA sequence in certain frame with the the potential to code for a protein. Because amino acids are coded by triplets of nucleotides, there are three possible frames to look … Continue reading

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BLAST from terminal against NCBI database using Perl

Using a Perl script you can BLAST your FASTA sequence file against the NCBI database directly from your terminal. The script is provided by the NCBI and you can download it here: ftp://ftp.ncbi.nlm.nih.gov/blast/documents/web_blast.pl The simple usage is: $ perl web_blast.pl … Continue reading

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