Difference between revisions of "Xenopus reference"

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(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).  
  
== v1. RefSeq of cDNA & protein ==
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== 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,  
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* 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.
  
 
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[[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

XENLA_cDNA_ref.v1.fasta

  • Used XenBase files: NcbiMrnaXenbaseGene_laevis.txt, xlaevisMRNA.fasta

XENLA_prot_ref.v1.fasta

  • Used XenBase files: NcbiProteinXenbaseGene_laevis.txt, xlaevisProtein.fasta
  1. Read gene name for each NCBI id from 'Ncbi...' file. Filter out genes with 'unnamed' in gene name field.
  2. Read all sequences from '.fasta' file. Convert all sequence character to upper case.
  3. If I find a sequence with '>gi|<gi number>|ref|<genbank accession>' header (means it is RefSeq entity), write it down.