We eliminated all conserved regions that coincide with the coding evidence provided by the UCSC data sets of mRNA, human spliced EST and human EST.
Another 36 FS antigens were human FS sequences (MS and mis-splicing FSs) that were also discovered from the human EST library analysis and were highly conserved in the dogs14.
A sequence homology search with the BLAST program showed that it had the highest homology (96.8% for the nucleotide sequences) to human chromosome 18pter-p11.23 clone 34 mRNA (Yoshikawa et al, 1997), a human EST.
At the time of analysis, the human EST sequences could be derived from 8618 EST libraries.
This isoform has been found as a human EST (DA392898) but is not present in the current rat databases.
Using this tool we mined the human EST (Expressed Sequence Tag) database for sequences derived exclusively from melanoma.
First, we searched human EST and cDNA databases and aligned corresponding ESTs with the genomic sequences of these caspase genes.
An example of such a scenario can be seen for the human EST corresponding to the Genbank accession BU608159.
The tool allows the mining of all available human EST data in a search for candidate genes with tissue restricted expression.
In order to quantitatively analyze the splicing pattern of an exon pair, we separately aligned each exon against the human EST database using BLAT [42].
Human EST sequences and their genomic alignments were retrieved from UCSC annotation database (March 11 , 2007update), and clustered into RefSeq loci as previously described [37].
