Hi,
I am looking for reasonable linear and affine gap penalties for local pairwise alignments of DNA and amino acid sequences. I am using the NUC and BLOSUM62 substitution matrices from NCBI, respectively.
The problem is, that a low penalty leads to very long alignments with many gaps (especially for DNA), that extend into non-homologous regions due to spurious matches.
In contrast, high penalties can lead to premature termination of alignments.
Can you give me some literature hints on how to find/calculate reasonable gap penalties? What are optimal penalties for the settings described above?
Hi.,
A Gap penalty is a method of scoring alignments of two or more sequences. When aligning sequences, introducing gaps in the sequences can allow an alignment algorithm to match more terms than a gap-less alignment can. ... Gap penalties are used to adjust alignment scores based on the number and length of gaps.
In addition, a method is needed to account for insertions and deletions that sometimes appear in related DNA or protein sequences. To accommodate such sequence variations, gaps that appear in sequence alignments are given a negative penalty score reflecting the fact that they are not expected to occur very often.Also there is a possibility of removing all the gaps within an alignment. In order to do this select "Edit -> Remove all gaps" in the multiple alignment editor right-click menu. On attached screenshots you can see an example of how to delete columns more than a half of which consist of gaps from an alignment.
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