The multisequence alignments where then aligned against the structure from their respective protein family.
Samples of fibres were aligned to produce film-textured alignments where all fibre axes are aligned parallel with the film plane.
Pindel [ 22] in version 0.1 requires uniquely and error-free mapped reads and allows only split read alignments where the read partners are aligned within two times the average insertion size.
CD alignments are block-wise multiple alignments where block regions are defined as those aligned among all family members.
Of these reciprocal hits, 6,942 sequences had alignments where 100% of the 'Prestige' transcript length aligned to the '378' transcript, or vice versa; these transcripts share the same protein length and sequencing reads covered the entire sequence length.
Partially correct alignments (where parts of a multiword expression are correctly aligned) are ignored.
In order to exclude poor alignments and reduce ambiguity, we filter out alignments where less than 85% of the RNA is aligned, or the sequence identity is less than 90%.
(ALIGN-M was not usable as it does not produce complete alignments where sequence tracts are too divergent).
This means that we are not interested in alignments where the corresponding splicing sites (one from each sequence) do not align exactly.
However, there are positions in the sequence alignments where there is a strong preference for the type of amino acid.
Alignments where the coverage was <0.96 of the length of the mRNA or EST and <98% sequence identity were discarded.
