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Ioanna Kalvari kalvari

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kalvari / fetch_species_seq_accs.sql
Created June 3, 2016 10:00
Fetch Rfam species sequence accessions by ncbi id
SELECT fr.rfam_acc, fr.rfamseq_acc
FROM full_region fr, rfamseq rs
WHERE fr.rfamseq_acc=rs.rfamseq_acc
AND fr.is_significant=1 AND rs.ncbi_id=6239 -- C.elegans
ORDER BY fr.rfam_acc;
@kalvari
kalvari / mammal_annotation.sql
Created March 31, 2016 14:53
Fetch all annotations for mammals
SELECT f.rfam_acc
from family f, family_ncbi fn, taxonomy tx
where f.rfam_acc=fn.rfam_acc
AND fn.ncbi_id=tx.ncbi_id
AND tax_string like '%Mammal%';
@kalvari
kalvari / 5SRNA_seqs_rfam_id.sql
Last active April 18, 2016 16:36
Retrieve 5S rRNA Rfam sequence selection using Rfam id
SELECT fr.rfamseq_acc
FROM full_region fr, family f
WHERE fr.rfam_acc=f.rfam_acc
AND f.rfam_id='5S_rRNA';
@kalvari
kalvari / 5SRNA_seqs_rfam_acc.sql
Last active April 18, 2016 16:36
Retrieve 5S rRNA Rfam sequence selection using family accession
SELECT rfamseq_acc
FROM full_region
WHERE rfam_acc='RF00001';
@kalvari
kalvari / fetch_plant_seqs.sql
Last active April 22, 2016 16:59
Retrieve Plant ncRNAs
SELECT fr.rfamseq_acc
FROM full_region fr, rfamseq rf, taxonomy tx
WHERE rf.ncbi_id=tx.ncbi_id
AND fr.rfamseq_acc=rf.rfamseq_acc
AND tx.tax_string LIKE '%Viridiplantae%';
@kalvari
kalvari / fetch_rat_seqs.sql
Last active April 25, 2016 13:59
Retrieve species specific Rfam sequence accessions
SELECT fr.rfam_acc, fr.rfamseq_acc, fr.seq_start, fr.seq_end
FROM full_region fr,rfamseq rf,taxonomy tx
WHERE rf.ncbi_id=tx.ncbi_id
AND fr.rfamseq_acc=rf.rfamseq_acc
AND tx.ncbi_id = 10116 -- ncbi tax id
AND fr.is_significant = 1;