[galaxy-user] Phylogenetic tree viewer ?

2011-05-13 Thread Luobin Yang
Hi, Do you guys know any phylogenetics tree viewer that works well with Galaxy system? Thanks, Luobin ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org.

[galaxy-user] finding Conserved non coding region

2011-05-13 Thread De Kumar, Bony
Hi all , I have a set of 1500 sequence obtained from my Chip_Seq experiment. I am interested to Know how many of them are within Conserved non coding Region. My definition of conserved Non coding region is as follows 1. Atleast a 200bp region with 80% conservation between Human , Mice and

[galaxy-user] UCSC-EMBOSS/fuzznuc-UCSC workflow?

2011-05-13 Thread Robert Curtis Hendrickson
Folks, I wanted to scan the 2kb upstream of a list of human gene isoforms for TFBS using fuzznuc. I was able to Get Data UCSC Main As sequence and get my sequences EMBOSS fuzznuc ran fine, and output the hits HOWEVER, fuzznuc lost the genomic position information that UCSC has put after a

[galaxy-user] Calling SNP's

2011-05-13 Thread sukeerthi teja Rallapalli
Hi, Is it possible to convert a fasta file to sam/bam format using galaxy. ? OR Is is possible to call SNP's using Blast 2.2.25 (Stand Alone Blast) Thank you Teja ___ The Galaxy User list should be used for the discussion of Galaxy