Tag Archives: sequence

Slackware and SlackBuilds.org cited in a scientific publication

The latest paper from our research group has just been published in Scientific Reports. A big part of the work was done in silico, using different software tools and databases. All bioinformatics software used locally was installed on a Slackware64 … Continue reading

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Cleaning up with sed 2

I have a list of nucleotide sequences in fasta format, obtained from NCBI. I want to clean the sequences names, leaving only the accession numbers. Additionally, I want to extract the accession numbers to a separate list. I am not … Continue reading

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FASTA syntax highlight

FASTA is among the most common text formats for nucleotide or amino acid sequences. I use medit and a feature that I have been looking for is a syntax highlighting for FASTA files. I want to have colour code for … Continue reading

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Converting sequences by squizz

Sometimes I need to have a DNA or amino acid sequence (or an alignment) in several different formats. A neat little program that can convert between different sequence formats is squizz. Its primary function is to serve as a sequence … Continue reading

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Geneconv: detect gene conversion

Geneconv is a program for detecting gene conversion between aligned DNA sequences. It can also search for gene conversion fragments from outside the alignment. The output results are ranked by P-values and presented in a spreadsheet manner. The data are … Continue reading

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