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What is the Impact of Adjusting the -reward Parameter in KMA Aligner?

I assume that the aligner uses terminology similar to Smith-Waterman Alignment. [Can't quickly find an explainer elsewhere, so I might as well write it out here in full...] In other words, each match ...
gringer's user avatar
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How can I include the start and end sequence number while doing MSA alignment with any alignment tool like CLUSTALW?

I'd recommend using ClustalX. You include the full length protein in each alignment along with the domain. The location of the domain from the start of the protein will then be automatically located. ...
M__'s user avatar
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How to align two FASTAs and extract the aligned part?

Given that you're aligning human mitochondrial DNA sequences, consider aligning each sequence to the Reconstructed Sapiens Reference Sequence (RSRS) as a base for alignment: http://phylotree.org/...
gringer's user avatar
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How to align two FASTAs and extract the aligned part?

When a phylogenetics calculation goes wrong the bug is almost certainly the alignment - so that bit of the question I understand. This suggests a machine learning algorithm is being used. In that case ...
M__'s user avatar
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Waterman-Smith-Beyer implementation in Python

This is simply the need for a gap penalty with the algorithm being used. Biopython has I believe a Waterman based aligner via Bio.pairwise2 and this should include a gap penalty. Lowering the gap ...
M__'s user avatar
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What is the best way to acquire protein isoform sequence alignment?

This is a paper that tries to address this problem "Splice-Aware Multiple Sequence Alignment of Protein Isoforms" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6508070/ I have not evaluated ...
Colin D's user avatar
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merging two/or more bed file into one bed file

To merge multiple BED files into one, you need to do the following: concatenate them all (bedtools merge only accepts one input BED) sort the concatenated BED ...
Michael Hall's user avatar

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