Chimeric sequences were identified by individually analyzing ESTs which joined alignments but included a sequence region that totally diverged from the rest of the alignment or those ESTs that were identified by BLAST as containing target sequences but did not join contigs.
Next, alignments were concatenated into a single pol alignment using the "Join Alignments" server [ 95].
All samples were included and batch processed using a zoom scan filter, three steps peak detector (local maxima mass detection, score connector chromatogram construction, Savitzky-Golay peak recognition) and alignment join aligner.
Therefore, neighbouring clones were joined by alignment with subject sequences obtained by a BLAST search.
Alignments of the sixth type 3 repeat or the C-terminal region (i.e. the type 3 repeats and L-lectin domain) were prepared by the progressive, neighborhood-joining alignment method, CLUSTALW [ 81].
It may be obtained by joining pairwise alignment graphs for all pairs of S-sequences.
In order to optimize the alignment, we align the domains separately and then join the alignments.
The pairwise alignments were joined to a multiple alignment with the roast program from the Threaded-Blockset-Aligner (TBA/MultiZ) [ 36].
The alignments were joined together by "Concatenate FASTA alignment by species" from the "FASTA manipulation" menu, and the alignment width was changed to 60-bp blocks by "FASTA Width formatter" from the "FASTA manipulation" menu.
At Cedar Street, NY 17D joined the modern alignment of NY 427.
