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 nucleotides and amino acids, similarly to how scripting or programming languages are displayed by the editor. I have been looking for this feature for a long time and all I found was the fasta.lang at GNOME’s wiki and the fastalang at git. Both projects are for Gedit and support only nucleotide sequences. Let’s say neither of these did the job for me, but I appreciate very much both projects. I decided to do things myself.
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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 format file checker, but can do some conversions. Read the rest of this entry »

ALINE: colouring, numbering and annotation

Aline is an extensible WYSIWYG protein sequence alignment editor for publication quality figures. It canĀ  read common sequence alignment formats which the user can then alter, embellish, markup etc to produce the kind of sequence figure commonly found in biochemical articles. Read the rest of this entry »

Protein MSA secondary structure

I needed to predict the secondary structure of amino acid sequences, already in a multiple sequence alignment (MSA). This means that the sequences had gaps, which could be a problem. I searched the net for a suitable, easy-to-use application or online server. Read the rest of this entry »

Amino acid sequence as a column

I need to present an amino acid sequence as a column, so I can paste it in a spreadsheet document (to serve as a reference to other analyses). There is a relatively straightforward way to do this. Read the rest of this entry »