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>sequence 4

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  1. >sequence 4 gccgaggctg cctgactgga atgagggtag ctgcggcgac tgcggcggct ggagcggggc cggccatggc ggtgtggacg cgggccacca aagcggggct ggtggagctg ctcctgaggg agcgctgggt ccgagtggtg gccgagctga gcggggagag cctgagcctg acgggcgacg ccgccgcggc cgagctggag cccgctctgg gacccgcggc cgccgccttc aacggcctcc caaacggcgg cggcgcgggc gactcgctgc ccgggagccc aagccgcggc ctggggcccc cgagcccgcc ggcgccgcct cggggccccg cgggtgaggc gggcgcgtcg ccgcccgtgc gccgggtgcg ggtggtgaag caagaggcgg gcggcctggg catcagcatc aagggcggcc gcgagaaccg gatgccgatc ctcatctcca agatcttccc cgggctggct gccgaccaga gccgggcgct gcggctgggc gacgccatcc tgtcggtgaa cggcaccgac ctgcgccagg ccacccacga ccaggccgtg caggcgctga agcgcgcggg caaggaggtg ctgctggagg tcaagttcat ccgagaagta acaccatata tcaagaagcc atcattagta tcagatctgc cgtgggaagg tgcagccccc cagtcaccaa gctttagtgg cagtgaggac tctggttcgc caaaacacca gaacagcacc aaggacagga agatcatccc tctcaaaatg tgctttgctg ctagaaacct aagcatgccg gatctggaaa acagattgat agagctacat tctcctgata gcaggaacac gttgatccta cgctgcaaag atacagccac agcacactcc tggttcgtag ctatccacac caacataatg gctctcctcc cacaggtgtt ggctgaactc aacgccatgc ttggggcaac cagtacagca ggaggcagta aagaggtgaa gcatattgcc tggctggcag aacaggcaaa actagatggt ggaagacagc aatggagacc tgtcctcatg gctgtgactg agaaggattt gctgctctat gactgtatgc cgtggacaag agatgcctgg gcgtcaccat gccacagcta cccacttgtt gccaccaggt tggttcattc tggctccgga tgtcgatccc cctcccttgg atctgacctt acatttgcta ccaggacagg ctctcgacag ggcattgaga tgcatctctt cagggtggag acacatcggg atctgtcatc ctggaccagg atacttgttc agggttgcca tgctgctgct gagctgatca aggaagtctc tctaggctgc atgttaaatg gccaagaggt gaggcttact attcactatg aaaatgggtt caccatctca agggaaaatg gaggctccag cagcatattg taccgctacc cctttgaaag gctgaagatg tctgctgatg atggcatccg aaatctatac ttggattttg gtggtcccga gggagaactg accatggacc tgcactcttg tccgaagccg attgtatttg tgttgcacac gtttttatcg gccaaagtca ctcgtatggg actgcttgta tgagcaacaa aaaatcagaa aagagccttg actgtcacaa gaaatatttc cacctcaaaa //

  2. Traduzione concettuale

  3. Basic Local Alignment Search Tool

  4. Peptide Sequence Databases • nrAll non-redundant GenBank CDS translations + RefSeq Proteins + PDB + SwissProt + PIR + PRF • refseqRefSeq protein sequences from NCBI's Reference Sequence Project. • swissprotLast major release of the SWISS-PROT protein sequence database (no updates). • patProteins from the Patent division of GenPept. • pdb Sequences derived from the 3-dimensional structure from Brookhaven Protein Data Bank. • monthAll new or revised GenBank CDS translation+PDB+SwissProt+PIR+PRF released in the last 30 days. • env_nrProtein sequences from environmental samples.

  5. Nucleotide Sequence Databases • nrAll GenBank + RefSeq Nucleotides + EMBL + DDBJ + PDB sequences (excluding HTGS0,1,2, EST, GSS, STS, PAT, WGS). No longer "non-redundant". • refseq_rnaRNA entries from NCBI's Reference Sequence project • refseq_genomicGenomic entries from NCBI's Reference Sequence project • estDatabase of GenBank + EMBL + DDBJ sequences from EST Divisions • est_humanHuman subset of est. • est_mouseMouse subset. • est_othersNon-Mouse, non-Human subset of est. • gssGenome Survey Sequence, includes single-pass genomic data, exon-trapped sequences, and Alu PCR sequences. • htgsUnfinished High Throughput Genomic Sequences: phases 0, 1 and 2 (finished, phase 3 HTG sequences are in nr) • patNucleotides from the Patent division of GenBank. • pdbSequences derived from the 3-dimensional structure from Brookhaven Protein Data Bank • monthAll new or revised GenBank + EMBL + DDBJ + PDB sequences released in the last 30 days. • dbstsDatabase of GenBank+EMBL+DDBJ sequences from STS Divisions . • chromosomeA database with complete genomes and chromosomes from the NCBI Reference Sequence project.. • wgsA database for whole genome shotgun sequence entries. • env_ntNucleotide sequences from environmental samples, including those from Sargasso Sea and Mine Drainage projects.

  6. Position-Specific Iterative (PSI) BLAST • Position-Specific Iterated (PSI)-BLAST is the most sensitive BLAST program, making it useful for finding very distantly related proteins. Use PSI-BLAST when your standard protein-protein BLAST search either failed to find significant hits, or returned hits with descriptions such as "hypothetical protein" or "similar to...".

  7. Position-Specific Iterative (PSI) BLAST • Prima fase: BLASTp con matrice di sostituzione più appropriata

  8. Position-Specific Iterative (PSI) BLAST

  9. Position-Specific Iterative (PSI) BLAST • Seconda fase: generazione di Position-Specific Similarity Matrix (PSSM) 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 A C D E F G H I K -8 9

  10. Position-Specific Iterative (PSI) BLAST

  11. Position-Specific Iterative (PSI) BLAST

  12. Pattern-Hit Initiated (PHI)-BLAST • Pattern-Hit Initiated (PHI)-BLAST is designed to search for proteins that contain a pattern specified by the user AND are similar to the query sequence in the vicinity of the pattern. This dual requirement is intended to reduce the number of database hits that contain the pattern, but are likely to have no true homology to the query. [LIVMF]-G-E-x-[GAS]-[LIVM]-x(5,11)-R-[STAQ]-A-x-[LIVMA]-x-[STACV]

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