Description

This track shows validated alignments of $organism mRNAs from the Mammalian Gene Collection (MGC) having full-length open reading frames (ORFs) to the genome.

Method

GenBank $organism MGC mRNAs identified as having full-length ORFs are aligned against the genome using the blat program. The Blat output is used to select the genomic location of the mRNA. The genomic sequence is then used for a refined alignment of the clone using several cDNA-to-genome programs. Clones are considered validated when
- all mismatches to the genome are either known SNPs or present in at least 8 other clones in the region
- the ORF of the mRNA can be verified using Twinscan (reference: I. Korf et al, Bioinformatics 2001).

When a single mRNA aligns in multiple places, it is currently discarded. This is an ongoing project: more clones will be validated in later stages.

For details on the clone alignments, see The Mammalian Genome Project at the WU-LCG

Credits

The MGC validated clones track is produced at the Brent Lab from mRNA sequence data submitted to GenBank by the Mammalian Gene Collection project.