Tag Archives: protein

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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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 … Continue reading

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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 … Continue reading

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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.

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