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/