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Question: Extracting Alignments From Multiz With Refseq Annotation
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gravatar for Vesselin Baev
10.7 years ago by
Vesselin Baev • 50
Vesselin Baev • 50 wrote:
Dear all, I'm wondering when I extract a alignments with coorfinates (for refseqs) from Multiz from genome-wide alignments I can make fasta MAFs with info-line with coordinates but never looking like this: 122200029 122200071 + 154141344 rn3.chr5 143135020 143135060 + 173106704 canFam1.chr15 6850518 6850559 + 67237905 CCTGCCCCTATTGTAAGTCAATTAATA-AAAAGAGCCATCTGG CTTGCCTCTATGATAAACCAGTTAATATAAAAGTGTCACATGG CTTGCCTCTGTTATAAGCCACTTAATA--AAAGTGTCACATGG CCTGCCTCTCATAGGAAGCAAGTAATG-AAAAGAGCCATCTGG 14280459 14280491 - 154141344 rn3.chr5 12802003 12802032 - 173106704 canFam1.chr2 5413700 5413729 - 87725193 GCCGGCCCAGCAAGATGAAACAG---GGCACCC GTCAGCCTGGGGGGGGTCGGCAGCCTGGCACCC GTCAGCCTGG---GAGTCGGCAGCCTGGCGCCC GCCAGCCCAGCAAGATGAAACAG---GGTGGCC How to make this? I have failed trying do this... Vesko -- 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
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modified 10.6 years ago by Daniel Blankenberg ♦♦ 1.7k • written 10.7 years ago by Vesselin Baev • 50
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gravatar for Daniel Blankenberg
10.6 years ago by
Daniel Blankenberg ♦♦ 1.7k
United States
Daniel Blankenberg ♦♦ 1.7k wrote:
Hi Vesko, I'm not sure what you are trying to do here. Let us know if you can provide more information about why you need this specific format arrangement. Dan
ADD COMMENT • link written 10.6 years ago by Daniel Blankenberg ♦♦ 1.7k
Hi, my task is automatically to make (not 1 by 1, namualy) an alignment of 3'UTRs of a 300 genes, I have the list of acc.numbers and/or names of them. When I do the MAFs I cannot see which blocks are from one UTR/gene/name.... Vesko 2008/4/16, Daniel Blankenberg <dan@bx.psu.edu>: -- 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
ADD REPLY • link written 10.6 years ago by Vesselin Baev • 50
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