Author: Hawkins, John A.; Kaczmarek, Maria E.; Müller, Marcel A.; Drosten, Christian; Press, William H.; Sawyer, Sara L.
Title: A metaanalysis of bat phylogenetics and positive selection based on genomes and transcriptomes from 18 species Document date: 2019_6_4
ID: telmxmp4_41
Snippet: The algorithm for finding best splice variant for a gene g in a given orthologous set S is as follows. First, find the consensus sequence of S from the MAFFT L-INS-i alignment. The consensus sequence is the identity in each column of the amino acid which is found in a majority of transcripts, or X if no single value is the majority. Next, align all splice variants of gene g against the consensus sequence, again using MAFFT L-INS-i, and score each.....
Document: The algorithm for finding best splice variant for a gene g in a given orthologous set S is as follows. First, find the consensus sequence of S from the MAFFT L-INS-i alignment. The consensus sequence is the identity in each column of the amino acid which is found in a majority of transcripts, or X if no single value is the majority. Next, align all splice variants of gene g against the consensus sequence, again using MAFFT L-INS-i, and score each by the number of nongap, non-X positions in agreement with the consensus. Select the splice variant with the highest score. This resulted in improved selection of 3,444 splice variants.
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