Difference between revisions of "Texas Xenopus Genome Project/Species Identification"
From Marcotte Lab
(Created page with '== How to select == * Download ''X. tropicalis'' mRNA sequences from XenBase (Nov. 27, 2009 version). ** xdata:ID/XENTR_mRNA.xenbase20091127.fasta.gz * Download CHORI-216 s...') |
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== How to select == | == How to select == | ||
* Download ''X. tropicalis'' mRNA sequences from XenBase (Nov. 27, 2009 version). | * Download ''X. tropicalis'' mRNA sequences from XenBase (Nov. 27, 2009 version). | ||
− | ** [[:xdata:ID/XENTR_mRNA.xenbase20091127.fasta.gz]] | + | ** [[:xdata:ID/XENTR_mRNA.xenbase20091127.fasta.gz]] 17 MB, gzipped. |
* Download CHORI-216 sequences (from XenBase) and CHORI-219 sequences (from NCBI GenBank). | * Download CHORI-216 sequences (from XenBase) and CHORI-219 sequences (from NCBI GenBank). | ||
− | ** [[:xdata:ID/XENTR_CH216.fasta.gz]] (CHORI-216 sequences. 160 BAC sequences from ''X. tropicalis'' genome) | + | ** [[:xdata:ID/XENTR_CH216.fasta.gz]] 1.2 MB, gzipped. (CHORI-216 sequences. 160 BAC sequences from ''X. tropicalis'' genome) |
− | ** [[:xdata:ID/XENLA_CH219.fasta.gz]] (CHORI-219 sequences. 29 BAC sequences from ''X. laeves'' genome) | + | ** [[:xdata:ID/XENLA_CH219.fasta.gz]] 6.5 MB, gzipped. (CHORI-219 sequences. 29 BAC sequences from ''X. laeves'' genome) |
* Run BLAT (with default option) to known CHORI BAC sequences. | * Run BLAT (with default option) to known CHORI BAC sequences. | ||
− | ** [[:xdata:ID/XENTR_mRNA.XENLA_CH219.blat_pslx.gz]] | + | ** [[:xdata:ID/XENTR_mRNA.XENLA_CH219.blat_pslx.gz]] 1.2 MB, gzipped. |
− | ** [[:xdata:XENTR_mRNA.XENTR_CH216.blat_pslx.gz]] | + | ** [[:xdata:XENTR_mRNA.XENTR_CH216.blat_pslx.gz]] 20 MB, gzipped. |
---- | ---- | ||
[[Category:XenopusGenome]] | [[Category:XenopusGenome]] |
Revision as of 10:53, 9 December 2009
How to select
- Download X. tropicalis mRNA sequences from XenBase (Nov. 27, 2009 version).
- xdata:ID/XENTR_mRNA.xenbase20091127.fasta.gz 17 MB, gzipped.
- Download CHORI-216 sequences (from XenBase) and CHORI-219 sequences (from NCBI GenBank).
- xdata:ID/XENTR_CH216.fasta.gz 1.2 MB, gzipped. (CHORI-216 sequences. 160 BAC sequences from X. tropicalis genome)
- xdata:ID/XENLA_CH219.fasta.gz 6.5 MB, gzipped. (CHORI-219 sequences. 29 BAC sequences from X. laeves genome)
- Run BLAT (with default option) to known CHORI BAC sequences.
- xdata:ID/XENTR_mRNA.XENLA_CH219.blat_pslx.gz 1.2 MB, gzipped.
- xdata:XENTR_mRNA.XENTR_CH216.blat_pslx.gz 20 MB, gzipped.