Difference between revisions of "Xenopus reference"
From Marcotte Lab
(→v1. RefSeq of cDNA & protein) |
(→v1. RefSeq of cDNA & protein) |
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All of these files are derived from XenBase (downloaded on May, 01, 2011). | All of these files are derived from XenBase (downloaded on May, 01, 2011). | ||
− | == | + | == Version 1. RefSeq of cDNA & protein == |
[[xdata:/xenbase/XENLA_cDNA_ref.v1.fasta|XENLA_cDNA_ref.v1.fasta]] | [[xdata:/xenbase/XENLA_cDNA_ref.v1.fasta|XENLA_cDNA_ref.v1.fasta]] | ||
* Used XenBase files: NcbiMrnaXenbaseGene_laevis.txt, xlaevisMRNA.fasta | * Used XenBase files: NcbiMrnaXenbaseGene_laevis.txt, xlaevisMRNA.fasta | ||
[[xdata:/xenbase/XENLA_prot_ref.v1.fasta|XENLA_prot_ref.v1.fasta]] | [[xdata:/xenbase/XENLA_prot_ref.v1.fasta|XENLA_prot_ref.v1.fasta]] | ||
− | * Used XenBase files: NcbiProteinXenbaseGene_laevis.txt, xlaevisProtein.fasta, | + | * Used XenBase files: NcbiProteinXenbaseGene_laevis.txt, xlaevisProtein.fasta |
+ | |||
+ | # Read gene name for each NCBI id from 'Ncbi...' file. Filter out genes with 'unnamed' in gene name field. | ||
+ | # Read all sequences from '.fasta' file. Convert all sequence character to upper case. | ||
+ | # If I find a sequence with '>gi|<gi number>|ref|<genbank accession>' header (means it is RefSeq entity), write it down. | ||
---- | ---- | ||
[[Category:XenopusGenome]] | [[Category:XenopusGenome]] |
Revision as of 12:13, 31 August 2011
All of these files are derived from XenBase (downloaded on May, 01, 2011).
Version 1. RefSeq of cDNA & protein
- Used XenBase files: NcbiMrnaXenbaseGene_laevis.txt, xlaevisMRNA.fasta
- Used XenBase files: NcbiProteinXenbaseGene_laevis.txt, xlaevisProtein.fasta
- Read gene name for each NCBI id from 'Ncbi...' file. Filter out genes with 'unnamed' in gene name field.
- Read all sequences from '.fasta' file. Convert all sequence character to upper case.
- If I find a sequence with '>gi|<gi number>|ref|<genbank accession>' header (means it is RefSeq entity), write it down.