Gene names were obtained by pairwise alignment to Refseq (m33 May 2005) and Ensembl (v31 May 2005) using megablast [ 47].
It should be pointed out that the present work only concerns (i) insertions and deletions among structural variations (not including copy-number variations such as segmental duplications; see ref. [13] for a review, and ref. [14]); and (ii) SNPs as detected by pairwise alignment of sequences.
Briefly, the mapping process includes mapping of RefSeq accessions to UniProtKB accessions using ID mapping services provided by Protein Information Resource and UniProt (40), followed by pairwise alignment of the sequences to map the positions.
Copies of Yq-linked genes were located within the currently-released draft sequence contigs [Mouse Chromosome Y Mapping Project (Jessica E. Alfoldi, Helen Skaletsky, Steve Rozen, and David C. Page at the Whitehead Institute for Biomedical Research, Cambridge MA, and the Washington University Genome Sequencing Center, St . Louis MO] by pairwise alignment of reference gene sequences to each contig.
To further examine the composition of the long MS4A proteins, each sequence was cut into its component subunits that were then compared to one another and to individual human MS4A sequences by pairwise alignment.
The resulting feline and bovine inhibitor nucleotide sequences were compared by pairwise alignment using a 2-sequence BlastN [ 28].
PpSP29 and PpSP32 share little homology between primary sequences by pairwise alignment (data not shown).
As detected by pairwise alignment (fig. 1), among the 19 mobile element insertions located in the aligned regions, ten insertions are clearly polymorphic between sequenced BAC inserts and, altogether, those insertions represent ∼70 kb of DNA insertions.
For 11 protein targets in our dataset, the sequence and structure similarity compared with those 30 background protein target structures can be calculated by pairwise alignment respectively.
Sequences greater than 97% identical, determined by pairwise alignment within the dataset, were also removed.
