Hello Valeria, We do not have a way to get the exact kind of output you describe.
If you are interested in having one record per gene you may find our knownCanonical table interesting. This table is generated in the following way (and can be obtained from the table browser as previously described): Given a cluster of transcripts (clustered according to overlapping exons), the transcript that has the most bases overlapping with other transcripts is selected as the canonical representative. If you would like to download the exons in this table (as a fasta file) along with other genomes aligned to them from our multiple alignment track you can find it here on our downloads page (for hg19): http://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz46way/alignments/ See: - knownCanonical.exon*.fa.gz: for each exon in the hg19/GRCh37 canonical set of UCSC Genes, this file contains either amino acids (AA) or nucleotides (Nuc) for hg19/GRCh37 and the aligning genomes. Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 11/24/10 09:23, Vasta, Valeria wrote: > Thank you will it condense repeated or overlapping exons for different > transcripts of a same gene? I would like to get the fasta from the > 5'most exon to the 3'-most one > > Vale > > -----Original Message----- > From: Brooke Rhead [mailto:[email protected]] > Sent: Tuesday, November 23, 2010 5:41 PM > To: Vasta, Valeria > Cc: [email protected] > Subject: Re: [Genome] (no subject) > > Hi Valeria, > > We do have one way to get this kind of output from the Table Browser, > but it is limited to use with gene tables. That is, it can't be used > directly with a custom track of coordinates. > > If you have a particular gene track in mind, select it in the Table > Browser (you can still intersect the gene table with a custom track of > coordinates, or paste a list of identifiers), then choose "CDS FASTA > alignment from multiple alignment" as the output type. > > After hitting "get output" you will see several options for formatting > the output, including whether to get amino acid or nucleotide sequence, > whether to separate the the FASTA file by exons, and which species from > the multiple alignment you would like included in the output. > > If you have further questions, please feel free to contact us again at > [email protected]. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 11/22/10 13:32, Vasta, Valeria wrote: >> Hello >> >> >> >> Can you kindly let me know how to get from genes coordinates to a >> multifasta file? >> >> thanks >> >> >> >> Valeria Vasta >> >> Assay Development Scientist | Biochemical and Molecular Genetics R&D >> >> Seattle Children's Research Institute >> >> 206-884-7674 OFFICE >> >> 206-987-7660 FAX >> >> [email protected] >> >> OFFICE 1900 9th Ave, Seattle, WA 98101 >> >> MAIL C9S-9 >> >> WWW seattlechildrens.org <http://seattlechildrens.org/> >> >> >> >> >> >> CONFIDENTIALITY NOTICE: This e-mail message, including any > attachments, is for the sole use of the intended recipient(s) and may > contain confidential and privileged information protected by law. Any > unauthorized review, use, disclosure or distribution is prohibited. If > you are not the intended recipient, please contact the sender by reply > e-mail and destroy all copies of the original message. >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is > for the sole use of the intended recipient(s) and may contain confidential > and privileged information protected by law. Any unauthorized review, use, > disclosure or distribution is prohibited. If you are not the intended > recipient, please contact the sender by reply e-mail and destroy all copies > of the original message. > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
