Hi Weimin, The answer to this question depends on what you are doing with the data is really up to you; however, you might want to take a look at our GenBank tracks to see what cutoffs we use for aligning mRNAs to the genome. From the "Pig mRNAs" track description:
-- Methods GenBank pig mRNAs were aligned against the genome using the blat program. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence were kept. -- And here are the less stringent rules that we use to align non-pig mRNAs to the pig genome: -- Methods The mRNAs were aligned against the pig genome using translated blat. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only those alignments having a base identity level within 1% of the best and at least 25% base identity with the genomic sequence were kept. -- If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 12/8/11 8:14 AM, dongdong zhaoweiming wrote: > Hi, > > I have a problem about determining gene structure in pig gene genome. > Generally speaking, we considered a sequence aligned to the genome if > hits that have> 95% identity across 90% of their length. But when > using BLAT, some of my sequence had a mutiposition,most of which had > two or three positions that meet the above criterion(some even have > both 100% identity and 100% length). So how should I define the > position? Should I always take the first one or take both? Thanks a > lot! > > Best regards！ weimin zhao > _______________________________________________ Genome maillist - > [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
