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NCBI
BLAST, 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.
tblastx
Compares the six-frame translations of a
nucleotide query sequence against the sixframe 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\IntrodBiolMolecCom
put20072\AULAS\FASTAsequence1.txt
BLAST
De 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 sequence
GTACCCTGAGCCCAGTCCCTACCTGCCTTCTGGAAGATGTTGGCTCCAGAATTCTCTGCCTCCCTCCTGC
AGGCATTGTGGCATTCACAGCTGATTTGCAGAGAGCCCAGATGCATCTCATAAATAAGGAATGTACTGTT
CTGCAGGACGGCTGTGGCGTGGCTGTGTGGGGGTGGGCAGGCTGGAGTAGACAGGAACCACGAGAGGCAG
GGAGGACTGTACAGGGGTTGCTGACCAGGTGGAAGATGATGGGAGCCTCAGAAGGTGTCGTGGGACAGGG
TCAGGGAGAGGGCTCTATGCGGCCAGGATCTGGATGCAGATTGTTGAGACTGAAATTTGGCTCAGATCCC
TTCTAGTTGTGTCTGTTTATCTTCAGTTTCCTTGTCTATAAAATGGGGAGAGATTGTGTGTCCCCGGCAT
CACTGGACTGTTAATAGCTATTGCATTTATAGCATTTATCCCAGAACCTGAAACACAGTAAATGCTCAGT
AAGTGTTATTATTTGCCCCAAACTGTCTTAGTGCTTTCCCCAAGAGCTTTGTGTTGTTTGTACTATGAGG
AATAATGAGGGTGGTGTGGGAGTCGGCCTCTGTGTCTGCAGAGAGGACCACAGGCCACAGGAATAGAGAC
AGGTAGATAGGATCAAGGTGACAGGAACAGATGTTCAGAGCAAGAGATGAAGACGGCATCATCAACCCAG
ACAAGCCAGGTAAGTCCCTGAAAGGGGACTGCATTTCTGCAGCCCTTTCAAGGTGGGCACTTGAGACATT
TGATTGGCTTTTAAAGGAAAGACTGACCTTTAGAAGGCATAAGCAGCTGGGGTCCCTGGAGACCCTGGGA
TGACACCGTCAGCATGGCTGTATTGAAACGGAGACCTCAGGCAAGCCACCTTTCTTCTCTGGGTCTCTGT
TCCATCTATAAAGTGCTTTCTGAGAAGCCCTCCAGAACCGCAGCATTGGAAGCTTCAAGATTTAGTCATT
CTTCTGGCAAACATATGTGGAAGGCCTCCGGGGTAGCACACCCTTCACCGTGCCCTGGAGATGCTGGGAT
GCGACAAAAAAGTAGGCTTCTCCCATGATGAACCTCACGGGTTAGTTGTGGGGGCGGCGGGGACGTGGGG
GGTGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATTGTGTACAACAGA
AAAGCAAATGGATATGTAATTCTAAACTGAAATCAGCCCCAGAAGGAGCGGGGCCCCAGTCAATCCAGGG
ACCTAAAAGTCAGGGAAGGTTCCCTGAAGACCATGAGGCTGGGCTGCTCCTGGAAGTGTGTGCCTGGGGT
Arquivos BLAST (Proteínas)
nr All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
month
All new or revised GenBank CDS
translation+PDB+SwissProt+PIR released in the
last 30 days.
swissprot
The 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 ests
The 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://ww
w.ncbi.nl
m.nih.gov/
Database/
NCBI - Conserved Domains Database
NCBI CDD
http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_h
elp.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/
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