Bioinformatics for DNA Sequence Analysis.pdf - Index of

Similarity Searching Using BLAST 11Table 1.4RefSeq categoriesExperimentally determinedand curatedGenome annotation (computationalpredictions from DNA)NCNGComplete genomic moleculesIncomplete genomic regionNM mRNA XM Model mRNANRRNA (non-coding)NP Protein XP Model proteinlllllllllNucleotide collection (nr/nt): contains INSDC + RefSeqnucleotides + PDB sequences, not including EST, STS, GSS,or unfinished HGT sequences. The nucleotide collection is themost comprehensive set of nucleotide sequences availablethrough BLAST.Reference mRNA sequences (refseq_rna): contains the nonredundantRefSeq mRNA sequences.Reference genomic sequences (refseq_genomic): containsthe non-redundant RefSeq genomic sequences.Expressed sequence tags (est): contains short, single readsfrom mRNA sequencing (via cDNA). These cDNA sequencesrepresent the mRNA in a cell at a particular moment in aparticular tissue.Non-human, non-mouse ESTs (est_others): the previousdatabase with human and mouse sequences removed.Genomic survey sequences (gss): contains random genomicsequences obtained from single-pass genome surveys, cosmids,BACs, YACs, and other survey methods. Their quality varies.High-throughput genomic sequences (HTGS): containssequences obtained from high-throughput genome centers.Sequences in this database contain a phase number, 0 beingthe initial phase and 3 being the finished phase. Once finished,the sequences move to the appropriate division in their respectivedatabase.Patent sequences (pat): contains sequences from the patentoffices at each of the INSDC organizations.Protein data bank (pdb): the nucleotide sequences from theBrookhaven Protein Data Bank managed by the Research Collaboratoryfor Structural Bioinformatics (http://www.rcsb.org/pdb).