Download presentation
Presentation is loading. Please wait.
Published byAldous Jones Modified over 9 years ago
1
NCBI BLAST, CDD, Mini-courses Katia Guimarães 2007/2
2
NCBI NCBI Entry Page: http://www.ncbi.nlm.nih.gov/http://www.ncbi.nlm.nih.gov/
3
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 http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
4
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.
5
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 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.
6
BLAST De volta à BLAST Entry Page: http://www.ncbi.nlm.nih.gov/blast/Blast.cgi http://www.ncbi.nlm.nih.gov/blast/Blast.cgi X:\public_html\cursos\grad\IntrodBiolMolecCom put20072\AULAS\FASTAsequence1.txt
7
BLAST De volta à BLAST Entry Page: http://www.ncbi.nlm.nih.gov/blast/Blast.cgi 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
8
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.
9
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.
10
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.
11
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.
12
NCBI - Databases NCBI CDD http://www.ncbi.nlm.nih.gov/Database/ Searching CDD http://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd
13
NCBI - Databases http://www.ncbi.nlm. nih.gov/D atabase/
14
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
15
NCBI - Mini cursos on-line NCBI Mini courses http://www.ncbi.nlm.nih.gov/Class/minicourses/
Similar presentations
© 2025 SlidePlayer.com. Inc.
All rights reserved.