NCBIBLAST, CDD, Mini-courses

Katia Guimarães

2007/2

NCBI

NCBI Entry Page: http://www.ncbi.nlm.nih.gov/

BLAST

BLAST = Basic Local Alignment Search Tool

Designed to take protein and nucleic acid sequences and compare them against a selection of NCBI databases. 

BLAST Entry Page: http://www.ncbi.nlm.nih.gov/blast/Blast.cgi

Selecting the BLAST Program

blastp Compares an amino acid query sequence against a protein sequence database.

blastn Compares a nucleotide query sequence against a nucleotide sequence database.

blastx Compares a nucleotide query sequence translated in all reading frames against a protein sequence database. You could use this option to find potential translation products of an unknown nucleotide sequence.

Selecting the BLAST Program

tblastn Compares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames.

tblastxCompares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database. Please note that the tblastx program cannot be used with the nr database on the BLAST Web page because it is computationally intensive.

BLAST

De volta à BLAST Entry Page: http://www.ncbi.nlm.nih.gov/blast/Blast.cgi

X:\public_html\cursos\grad\IntrodBiolMolecComput20072\AULAS\FASTAsequence1.txt

BLASTDe volta à BLAST Entry Page: http://www.ncbi.nlm.nih.gov/blast/Blast.cgi>ref|NC_000022.9|NC_000022:25372215-25392899 Homo sapiens chromosome 22, reference assembly, complete sequenceGTACCCTGAGCCCAGTCCCTACCTGCCTTCTGGAAGATGTTGGCTCCAGAATTCTCTGCCTCCCTCCTGCAGGCATTGTGGCATTCACAGCTGATTTGCAGAGAGCCCAGATGCATCTCATAAATAAGGAATGTACTGTTCTGCAGGACGGCTGTGGCGTGGCTGTGTGGGGGTGGGCAGGCTGGAGTAGACAGGAACCACGAGAGGCAGGGAGGACTGTACAGGGGTTGCTGACCAGGTGGAAGATGATGGGAGCCTCAGAAGGTGTCGTGGGACAGGGTCAGGGAGAGGGCTCTATGCGGCCAGGATCTGGATGCAGATTGTTGAGACTGAAATTTGGCTCAGATCCCTTCTAGTTGTGTCTGTTTATCTTCAGTTTCCTTGTCTATAAAATGGGGAGAGATTGTGTGTCCCCGGCATCACTGGACTGTTAATAGCTATTGCATTTATAGCATTTATCCCAGAACCTGAAACACAGTAAATGCTCAGTAAGTGTTATTATTTGCCCCAAACTGTCTTAGTGCTTTCCCCAAGAGCTTTGTGTTGTTTGTACTATGAGGAATAATGAGGGTGGTGTGGGAGTCGGCCTCTGTGTCTGCAGAGAGGACCACAGGCCACAGGAATAGAGACAGGTAGATAGGATCAAGGTGACAGGAACAGATGTTCAGAGCAAGAGATGAAGACGGCATCATCAACCCAGACAAGCCAGGTAAGTCCCTGAAAGGGGACTGCATTTCTGCAGCCCTTTCAAGGTGGGCACTTGAGACATTTGATTGGCTTTTAAAGGAAAGACTGACCTTTAGAAGGCATAAGCAGCTGGGGTCCCTGGAGACCCTGGGATGACACCGTCAGCATGGCTGTATTGAAACGGAGACCTCAGGCAAGCCACCTTTCTTCTCTGGGTCTCTGTTCCATCTATAAAGTGCTTTCTGAGAAGCCCTCCAGAACCGCAGCATTGGAAGCTTCAAGATTTAGTCATTCTTCTGGCAAACATATGTGGAAGGCCTCCGGGGTAGCACACCCTTCACCGTGCCCTGGAGATGCTGGGATGCGACAAAAAAGTAGGCTTCTCCCATGATGAACCTCACGGGTTAGTTGTGGGGGCGGCGGGGACGTGGGGGGTGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATTGTGTACAACAGAAAAGCAAATGGATATGTAATTCTAAACTGAAATCAGCCCCAGAAGGAGCGGGGCCCCAGTCAATCCAGGGACCTAAAAGTCAGGGAAGGTTCCCTGAAGACCATGAGGCTGGGCTGCTCCTGGAAGTGTGTGCCTGGGGT

Arquivos BLAST (Proteínas)nr All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF 

monthAll new or revised GenBank CDS translation+PDB+SwissProt+PIR released in the last 30 days. 

swissprotThe last major release of the SWISS-PROT protein sequence database (no updates). These are uploaded to our system when they are received from EMBL.

Arquivos BLAST (Proteínas)patents Protein sequences derived from the Patent division of GenBank.

Yeast Yeast (Saccharomyces cerevisiae) protein sequences. This database is not to be confused with a listing of all Yeast protein sequences. It is a database of the protein translations of the Yeast complete genome.

E. Coli E. coli (Escherichia coli) genomic CDS translations.

PDB Sequences derived from the 3-dim structure Brookhaven Protein Data Bank.

Arquivos BLAST (DNA)

nr All non-redundant GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS, or HTGS seqs).

month All new or revised GenBank+EMBL+DDBJ+ PDB sequences released in the last 30 days.

dbest Non-redundant database of GenBank+EMBL+DDBJ EST Divisions.

mouse ests The non-redundant Database of GenBank+EMBL+DDBJ EST Divisions limited to the organism mouse.

Arquivos BLAST (DNA)human ests The Non-redundant Database of GenBank+EMBL+DDBJ EST Divisions limited to the organism human.

other estsThe non-redundant database of GenBank+EMBL+DDBJ EST Divisions all organisms except mouse and human.

Yeast Yeast (Saccharomyces cerevisiae) genomic nucleotide sequences. Not a collection of all Yeast nucelotides sequences, but the sequence fragments from the Yeast complete genome.

NCBI - Databases

NCBI CDD

http://www.ncbi.nlm.nih.gov/Database/

Searching CDD

http://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd

NCBI - Databases

http://www.ncbi.nlm.nih.gov/Database/

NCBI - Conserved Domains Database

NCBI CDD

http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml

Searching CDD

http://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd

NCBI - Mini cursos on-line

NCBI Mini courses

http://www.ncbi.nlm.nih.gov/Class/minicourses/