The block borders will happen if there is a gap on EITHER side, query or target (and sometimes both sides).
Often gaps are one-sided. In the case of mRNA, most of the gaps will be on the query side, corresponding to the introns. In addition to blocks that match, there might be ends that do not align. For instance, on MRNA, you may have a AAAAAA-tail that does not align. Sometimes there are stretches of dna on the query and target which simply do not align with each other, and might be of different sizes, but surrounded by aligning regions. We call this a double-sided gap. There is a lower-level cutoff of 20 on hgBlat where 2 blocks with a gap smaller than that will be merged in the output display. -Galt Ar 7/4/2010 6:15 PM, scríobh 林宣佑(Hsuan-Yu Lin): > Thanks your replay! > > So, in the blat output format, the Q gap count is equal to qNumInsert which > from > documentation? > > And in the Blat output format, if the block count is 5 , > Can I say which exist 4 indel in this gene region? > > > ===================================== > Hsuan-Yu Lin > Division of Biostatistics and Bioinformatics, Institute of Population Health > Sciences, NHRI. > 35, Keyan Road, Zhunan Town, Miaoli County 35053, Taiwan, ROC > e-mail：[email protected] > TEL：(886)-37-246166 ext. 36187 > FAX：(886)-37-586467 > > -----Original message----- > From:Galt Barber<[email protected]> > To:[email protected] > Cc:genome<[email protected]> > Date:Fri, 02 Jul 2010 11:20:08 -0700 > Subject:Re: [Genome] Question about Blat output format > > > Hi, Yuan! > > This is no new change. > It has been that way since 2001. > > You are right that the documenation names the columns > according to the actual field names in the .h program structure. > > But when blat tools and programs output the PSL header, > it uses a more human-friendly format. > > There is no change in meaning or behavior between > the documentation and the actual PSL header produced. > > -Galt > > 林宣佑(Hsuan-Yu Lin) wrote: >> Hi~ >> >> The Blat default format list is like : >> >> 1. matches - Number of bases that match that aren't repeats >> 2. misMatches - Number of bases that don't match >> 3. repMatches - Number of bases that match but are part of repeats >> 4. nCount - Number of 'N' bases >> 5. qNumInsert - Number of inserts in query >> 6. qBaseInsert - Number of bases inserted in query >> 7. tNumInsert - Number of inserts in target >> 8. tBaseInsert - Number of bases inserted in target >> ..... >> ( from http://genome.ucsc.edu/FAQ/FAQformat.html#format2 ) >> >> But in the real output format, not exist any insert information, but exist >> gap information, like: >> >> 5. qNumInsert ---> Q gap count >> 6. qBaseInsert ---> Q gap bases >> ----- >> >> Is it the new PSL format? >> >> Any in the Blat output format, we can know block count. >> If there is 5 block count, Can I say which exist 4 indel in this gene region? >> >> >> Thank you ! >> >> >> ===================================== >> Hsuan-Yu Lin >> Division of Biostatistics and Bioinformatics, Institute of Population Health >> Sciences, NHRI. >> 35, Keyan Road, Zhunan Town, Miaoli County 35053, Taiwan, ROC >> e-mail：[email protected] >> TEL：(886)-37-246166 ext. 36187 >> FAX：(886)-37-586467 >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
