Parfrey Euk Markers – Accessions to GIs to Taxon IDs

Spent today wrestling with scripts to convert these damn accessions to GI numbers; Guillaume modified some of the BioPerl scripts using Bio::DB::Eutils modules. All listed in Edhar: /home/hollybik/eukmarkers_taxonids/accs_from_aligns/

Run the following commands to convert Accessions to GIs and then pull down NCBI taxon IDs (script prints text output with Accession GI NCBI_taxon with space between each)

perl Accs_14_3_3 Taxon_gi_14_3_3
perl Accs_40S Taxon_gi_40S
perl Accs_Actin Taxon_gi_Actin
perl Accs_Atub Taxon_gi_Atub
perl Accs_Btub Taxon_gi_Btub
perl Accs_ef1aLike Taxon_gi_ef1aLike
perl Accs_ef2 Taxon_gi_ef2
perl Accs_enolase Taxon_gi_enolase
perl Accs_gamma Taxon_gi_gamma
perl Accs_grc5 Taxon_gi_grc5
perl Accs_hsp70 Taxon_gi_hsp70
perl Accs_hsp70cyt Taxon_gi_hsp70cyt
perl Accs_hsp70er Taxon_gi_hsp70er
perl Accs_Hsp90 Taxon_gi_Hsp90
perl Accs_metk Taxon_gi_metk
perl Accs_Rad51 Taxon_gi_Rad51
perl Accs_rps22 Taxon_gi_rps22
perl Accs_Rps23a Taxon_gi_Rps23a
perl Accs_TFIIH Taxon_gi_TFIIH
perl Accs_Tsec61 Taxon_gi_Tsec61
perl Accs_U5 Taxon_gi_U5


Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

%d bloggers like this: