Vasko,
Due to the nature of the MAF format, a single genomic interval can be covered by more than one MAF block. There is currently no method of naming individual blocks.
You may want to take a look at the Stitch MAF Blocks tool to get one FASTA alignment block per input region from your MAF alignment.
Additional information on MAF tools can be found here: http://g2.trac.bx.psu.edu/wiki/MAFanalysis
Dan
Dear all, I heve done this in steps:
- Go to genome.ucsc.edu and select the tables link.
- Select the clade, organism, and assembly that you are interested in.
- Select Genes and Gene Predictions from the group.
- Select UCSC genes from track.
- From region select genome.
-from Paste List I put my needed list of genes. 6. From output format select custom track. 7. Select get output. 8. On that page put in utr3 in the name, and select 3' UTR exons. 9. Select get custom track in table browser. 10. Select Comparative Genomics from group. 11. Select Conservation from track 12. Select 28-multiz from table. 13. Click on the create button in the intersection line. 14. Select Custom Tracks from the group. 15. Select utr3 from the track.
for example I have 100 genes (in Paste List) that I get UTRs from them and use in intersection line. I got MAFs that exceed 100 pieces, every MAF have coordinates, but how to see which MAF blocks are for the first UTR (of some gene)? is there a way to name the MAF blocks?
Vesko
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Dr. Vesselin Baev University of Plovdiv Dept. Molecular Biology Bioinformatics Group Tzar Assen 24 Plovdiv 4000, BULGARIA 032/ 261 (534) 089/ 43 80 945 Skype: vesselin_baev vebaev@gmail.com baev@uni-plovdiv.bg _______________________________________________ galaxy-user mailing list galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user