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
