Codon 1, 2 and 1+2 sequences were extracted from CDS alignments and used as input for building trees, along with protein and CDS sequences.
Four sequences were extracted from GivenImaging capsule videos [4].
Candidate sequences were extracted from the 50 most highly upregulated genes from the microarray analyses.
Only continuous sequences were extracted from genomes.
These sequences were extracted and aligned using ClustalW.
Individual protein sequences were extracted from SWISSPROT database (release 55.0) (http://www.SwissProt.org) using protein IDs.
Individual colorspace sequences were loaded into a MySQL database from which distinct colorspace sequences were extracted.
Spacer sequences were extracted from both genomes using perl script software.
8,998 paired SK/RR sequences were extracted from 769 fully sequenced bacterial genomes (see Methods).
The 16 T. thynnus sequences were extracted from the study by Alvarado Bremer et al. [15].
Sets of sequences were extracted from each of the all_mrna, stsMap, and all_est annotation tables.
