Difference between revisions of "Xenopus reference"
From Marcotte Lab
(→Version 1. RefSeq of cDNA & protein) |
|||
| Line 2: | Line 2: | ||
== Version 1. RefSeq of cDNA & protein == | == Version 1. RefSeq of cDNA & protein == | ||
| + | # 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. | ||
| + | |||
[[xdata:/xenbase/XENLA_cDNA_ref.v1.fasta|XENLA_cDNA_ref.v1.fasta]] (8,879 sequences) | [[xdata:/xenbase/XENLA_cDNA_ref.v1.fasta|XENLA_cDNA_ref.v1.fasta]] (8,879 sequences) | ||
* Used XenBase files: NcbiMrnaXenbaseGene_laevis.txt, xlaevisMRNA.fasta | * Used XenBase files: NcbiMrnaXenbaseGene_laevis.txt, xlaevisMRNA.fasta | ||
| Line 8: | Line 12: | ||
* Used XenBase files: NcbiProteinXenbaseGene_laevis.txt, xlaevisProtein.fasta | * Used XenBase files: NcbiProteinXenbaseGene_laevis.txt, xlaevisProtein.fasta | ||
| − | + | ||
| − | + | ||
| − | + | ||
---- | ---- | ||
[[Category:XenopusGenome]] | [[Category:XenopusGenome]] | ||
Revision as of 12:16, 31 August 2011
All of these files are derived from XenBase (downloaded on May, 01, 2011).
Version 1. RefSeq of cDNA & protein
- 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.
XENLA_cDNA_ref.v1.fasta (8,879 sequences)
- Used XenBase files: NcbiMrnaXenbaseGene_laevis.txt, xlaevisMRNA.fasta
XENLA_prot_ref.v1.fasta (8,878 sequences; 'taf5' is not annotated as RefSeq in protein, although its corresponding mRNA sequence is annotated as RefSeq.)
- Used XenBase files: NcbiProteinXenbaseGene_laevis.txt, xlaevisProtein.fasta
