Genomic Sequence

Genomic Sequence

Postby soliu » 02 Jun 2015 11:13

I wonder where I can get the genomic sequence (fasta format with chromosome name and coordianates in the description line) for Xenopus Laevis? We are doing a relatively large scale project and need the database for alignment in our own computer.
Also we will need annotation information to identify the genes with the chromosome coordinates. When we worked on data from mouse and human, we can get such information by Biomart from Ensembl, but Xenopus Laevis is not available from Ensembl.
Thanks,
soliu
 
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Re: Genomic Sequence

Postby xenbase » 24 Jun 2015 12:20

Did you look at the xenbase ftp page?

http://www.xenbase.org/other/static/ftpDatafiles.jsp

there are FASTA files for both X laevis and X tropicalis.
xenbase
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Re: Genomic Sequence

Postby soliu » 25 Jun 2015 15:12

I looked at the fasta files, but did not find a file containing the genomic sequence with genomic coordinates.
I wonder if the XLv80 genome sequences are available for downloading?
soliu
 
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