Hello, For this linked alignment, the blue colored bases represent those that are in the alignment. This is unrelated to masking.
For the previous alignment, when I said: "the "+" means that the data are compatible but differ (in this case by being soft-masked/unmasked between the query/target)" I mean that the "|" is the same as an exact match, same base, same state of masking. And that the "+" is also considered a match, but a different kind of match. Not the same as an exact match (above) because even though they are the same base (i.e. compatible, to be interpreted as a match) they differ in the state of masking (one is masked, the other unmasked). I hope this helps to clarify the data, Jennifer Jackson UCSC Genome Bioinformatics Group Pattle Pun wrote: > ** High Priority ** > > Dear Jennifer, > > I checked your BLAT disply with the attached sequence. The alignment returned > was > > http://genome.ucsc.edu/cgi-bin/hgc?o=44661&g=htcUserAli&i=../trash/hgSs/hgSs_genome_669d_a14950.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_669d_a14950.fa+hg18_snp129_rs10399749&c=chr1&l=44661&r=45662&db=hg18&hgsid=122382550 > > It only has upper cases and blue colors and did not have the "|" and the "+" > signs. > > I still have several queestions: > > (1) Are upper cases and blue colors equal to your "soft-masked" and lower > cases equal to your unmasked. > > (2) I do not understand what is meant by "the "+" means > that the data are compatible but differ (in this case by being > soft-masked/unmasked between the query/target)". How can they be compatible > (the same) and yet different? > > Pattle.P.T.Pun, Ph.D. > Professor of Biology, > Wheaton College, > Wheaton, IL 60187 > phone: 630-752-5303 > fax: 630-752-5996 > email: [email protected] > http://www.wheaton.edu/Biology/faculty/ppp/index.html > >>>> Jennifer Jackson <[email protected]> 02/16/09 1:47 PM >>> >>>> > Hello, > What you are noticing is the display conventions used for Blat > alignments. If both bases are compatible (the same) and are soft-masked > or unmasked at the same position, the alignment will have a "|" between > the bases. If one is soft-masked and the other unmasked, the "+" means > that the data are compatible but differ (in this case by being > soft-masked/unmasked between the query/target). If you should come > across a <blank space> that would mean that the bases are not > compatible. If you see a "." dot in one of the sequences instead of a > base (atcgn/ATCGN), it represents a gap (a missing base in the sequence > within the context of the alignment block), perhaps pointing to a > deletion or an insertion event, depending on which sequence is > considered the reference. > I hope this helps to describe the data. Please let me know if I have > misunderstood your question, > Thank you, > Jennifer Jackson > UCSC Genome Bioinformatics Group > > > Pattle Pun wrote: > >> ** High Priority ** >> ** Reply Requested When Convenient ** >> >> What are the differences between perfect alighments in your realignment page >> of SNP below: i.e. >> >> http://genome.ucsc.edu/cgi-bin/hgc?hgsid=122295935&o=45161&t=45162&g=snp129&i=rs10399749&c=chr1&l=44911&r=45412&db=hg18&pix=800 >> >> Here the alignments in lower cases only or in upper cases only are perfect >> as well as those in lower case with upper cases. However, those latter >> alignments are shown with + signs. Why? >> >> Pattle.P.T.Pun, Ph.D. >> Professor of Biology, >> Wheaton College, >> Wheaton, IL 60187 >> phone: 630-752-5303 >> fax: 630-752-5996 >> email: [email protected] >> http://www.wheaton.edu/Biology/faculty/ppp/index.html >> >> _______________________________________________ >> Genome maillist - [email protected] >> http://www.soe.ucsc.edu/mailman/listinfo/genome >> >> > > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
