Hello, In the description of this track it states:
"To be considered spliced, an EST must show evidence of at least one canonical intron, i.e. the genomic sequence between EST alignment blocks must be at least 32 bases in length and have GT/AG ends." BLAT is used to generate the alignments and it starts a new block whenever there is an indel. So you can end up with a PSL that looks like it has two adjacent blocks in the genome sequence because there is an insertion in the mRNA (i.e. a deletion in the genome sequence). Thus there can be additional gaps in the alignments (in addition to the minimum 'one canonical intron') due to indels. Often sequencing error or polymorphism can cause indels. Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 04/06/11 08:38, HE Liu,Student wrote: > hi guys: > > this is probably a really stupid question, but it do confuse me... > > based on the description of SpilcedEST track: > the genomic sequence between EST alignment > blocks must be at least 32 bases in length and have GT/AG ends. > and by a simply checking, i find that substantial proportion of distances > between 2 neighboring alignment blocks of an EST sequence is less or equal > than 1, doesn't this mean these 2 neighboring blocks are actually continuous > region? if they are, why would them be 2 blocks? > by the description, it sounds like alignment blocks are exons... or i > misunderstand these blocks are just produced by Blat, and i need to check > canonical GT/AT sites from genome sequence in order to get right exon-intron > structures? > > Thanks~~ > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
