Your helper for a reasonable work with multiple sequence alignments (in bioinformatics)
This software is aimed to help in a daily routine work of a bioinformatician who works with multiple sequence alignments and uses them further to build phylogenetic trees. Briefly, it is a graphical interface which allows to maintain multiple projects with sequence alignment and additional data for it. First, it can map information about hits of profile HMMs from a certain database on the sequence alignment, including predictions of transmembrane helices. Also it can be used to remove poorly aligned or truncated sequences in semi-automated mode. Finally, as a small cherry on top, it has a sequence format converter which allows to convert all main sequence formats (NCBI, Uniprot, PDB etc) into more convenient format for working with multiple alignment and phylogenetic tree.
Please visit our web page for other bioinformatical tools and more info: http://boabio.belozersky.msu.ru/en/scientific-group
Current version of Alnalyser works with Python3+ and Tkinter. Last version supporting Python 2.7 was 1.0.3.
One (questionable) feature of this piece of software is that it does NOT utilize specific bioinformatical python modules (like biopython), but instead in several steps it uses native binary programs.
- muscle (https://drive5.com/muscle/downloads_v3.htm) - for multiple alignment (use version 3.8.31)
- hmmbuild, hmmsearch and hmmscan from HMMer (http://hmmer.org/) - for similary searches with profiles
In order to work with the 'Features' tab, which from my point of view is a very nice idea, one should have two databases of sequence profiles:
- Pfam (get a release from here: https://www.ebi.ac.uk/interpro/download/pfam/)
- COG (look for a link "Download all COGs profile HMMs" here: http://boabio.belozersky.msu.ru/en/tools)
As mentioned above, Alnalyser can store and work out information about transmembrane helices predictions in the format given by the DeepTMHMM (https://dtu.biolib.com/DeepTMHMM). Please use the .gff3 output format and copy the result into the corresponding window.
You can run Alnalyser with a settings filename as a single argument. For example:
python Alnalyser.py dummy_settings.ini
If the script is opened without any argument, it will try to load settings from the file settings.ini.
Creation of this tool was supported by the Dmitry Zimin's Dynasty Foundation, grant for young biologists, 2014