NCBI FieldGuide NCBI Molecular Biology Resources Part 2 November 2008 Peter Cooper

NCBI FieldGuide Genomic Resources NCBI BLAST NCBI Resources: Part 2

NCBI FieldGuide Genome Resources

NCBI FieldGuide Complete Genomes including draft assemblies, Oct 2008 Organisms: Viruses (2,187) Archaea (60) Bacteria (1,284) Eukaryotes (191) Organelles: Mitochondria (1,537) Plastids (147)

NCBI FieldGuide Higher Eukaryotic Genomes Oct 2008 Animals (78) –Placozoa (1) –Cnidaria (2) –Nematodes (7) –Mollusks (1) –Arthropods (23) Insects (21) Crustaceans (1) Arachnids (1) –Echinoderms (1) –Chordates (42) Fungi (57) –Ascomycetes (58) –Basidiomycetes (9) Land Plants –Angiosperms (7) –Mosses (1) metazoa[organism] OR dikarya[organism] OR streptophyta[organism] 153 Total species

NCBI FieldGuide Genome Resources: All Genomes

NCBI FieldGuide Eukaryotic Genomes Only

NCBI FieldGuide Microbial Genomes Only: COGs and Protein Clusters

NCBI FieldGuide Selected Eukaryotic Genomes

NCBI FieldGuide NM_000249: Genome Links

NCBI FieldGuide Map Viewer: MLH1 Customizable NCBI Assembly EST Hits Gene Annotations Models Transcripts Download data and sequences

NCBI FieldGuide Maps and Options

NCBI FieldGuide Mapped Variations

NCBI FieldGuide Synteny: Mammalian Genomes Albumin Gene Family

NCBI FieldGuide The New Homologene early globin gene A-chain gene B-chain gene frog A chick A mouse Amouse B chick B frog B paralogs orthologs gene duplication No longer UniGene based Protein similarities first Guided by taxonomic tree Includes orthologs and paralogs No longer UniGene based Protein similarities first Guided by taxonomic tree Includes orthologs and paralogs

NCBI FieldGuide Finding Homologs: HomoloGene Gene Provides Neighboring Function Gene

HomoloGene Cluster

NCBI FieldGuide Expanded Coverage: UniGene Fathead Minnow MLH1

HomoloGene Downloader Protein mRNA Genomic Protein mRNA Genomic

NCBI FieldGuide Microbial Genomes

NCBI FieldGuide E. coli mutL Gene Record

NCBI FieldGuide Entrez Genomes View

NCBI FieldGuide New Sequence Viewer (All Genomes)

NCBI FieldGuide Incipient Genome Browser

NCBI FieldGuide COGs Analysis E.Coli K12 Genome

NCBI FieldGuide Protein Clusters (Update for COGs) Genomic order

NCBI FieldGuide Sequence Similarity Searching Basic Local Alignment Search Tool

NCBI FieldGuide The Flavors of BLAST Position independent scoring –Standard BLAST traditional contiguous word hit nucleotide, protein and translations –Megablast can use discontiguous words nucleotide only optimized for large batch searches Position dependent scoring –PSI-BLAST constructs PSSMs automatically searches protein database with PSSMs –RPS BLAST searches a database of PSSMs basis of conserved domain database

NCBI FieldGuide Basic BLAST: Databases

NCBI FieldGuide BLAST Databases: Non-redundant protein nr ( non-redundant protein sequences ) –GenBank CDS translations –NP_, XP_ RefSeqs –Outside Protein PIR, Swiss-Prot, PRF PDB (sequences from structures) pat protein patents env_nr environmental samples nr ( non-redundant protein sequences ) –GenBank CDS translations –NP_, XP_ RefSeqs –Outside Protein PIR, Swiss-Prot, PRF PDB (sequences from structures) pat protein patents env_nr environmental samples Services blastp blastx

NCBI FieldGuide Nucleotide Databases: Human and Mouse Human and mouse genomic and transcript now default Separate sections in output for mRNA and genomic Direct links to Map Viewer for genomic sequences Megablast, blastn service

NCBI FieldGuide Nucleotide Databases: Traditional Services blastn tblastn tblastx

NCBI FieldGuide Nucleotide Databases: Traditional nr (nt) –Traditional GenBank –NM_ and XM_ RefSeqs refseq_rna refseq_genomic –NC_ RefSeqs dbest –EST Division est_human, mouse, others htgs –HTG division gss –GSS division wgs –whole genome shotgun env_nt –environmental samples Databases are mostly non-overlapping

NCBI FieldGuide WWW BLAST

NCBI FieldGuide WWW BLAST Interface

NCBI FieldGuide The BLAST homepage New URL:

NCBI FieldGuide Universal Form: Protein

NCBI FieldGuide Universal Form: Nucleotide Speed Sensitivity More Less More

NCBI FieldGuide Limiting Database: Organism Organism autocomplete

NCBI FieldGuide Limiting Database: Entrez Query all[filter] NOT mammals[organism] gene_in_mitochondrion[Properties] 2006:2007 [Modification Date] Nucleotide biomol_mrna[Properties] biomol_genomic[Properties] all[filter] NOT mammals[organism] gene_in_mitochondrion[Properties] 2006:2007 [Modification Date] Nucleotide biomol_mrna[Properties] biomol_genomic[Properties]

NCBI FieldGuide Algorithm parameters: Protein Adjust to set stringency May limit results Default statistics adjustment for compositional bias Default statistics adjustment for compositional bias Off now by default. Conflicts with comp-based stats Off now by default. Conflicts with comp-based stats Expand

NCBI FieldGuide Automatic Short Sequence Adjustment e-value Word Size 2 MatrixPAM30 Comp Stats Off Low Comp FilterOff Nucleotide and Protein

NCBI FieldGuide Algorithm parameters: Nucleotide blastn Masks species-specific interspersed repeats Essential for genomic query sequences Masks species-specific interspersed repeats Essential for genomic query sequences Prevents starting alignment in masked region Allows extensions through masked regions Prevents starting alignment in masked region Allows extensions through masked regions Masks LC sequence (simple repeats)

NCBI FieldGuide BLAST Formatting Options

NCBI FieldGuide Formatting Page (Now on Results) Alignment View Pairwise Pairwise with dots for identities Query-anchored with dots for identities Query-anchored with letters for identities Flat query-anchored with dots for identities Flat-query anchored with letters for identities Alignment View Pairwise Pairwise with dots for identities Query-anchored with dots for identities Query-anchored with letters for identities Flat query-anchored with dots for identities Flat-query anchored with letters for identities

NCBI FieldGuide Download Options (Now on Results) Structured Formats Saved Settings Reusable on Web Portable to Standalone PSSM Reusable on Web Portable to Standalone Standalone formatter (future)

NCBI FieldGuide Structured formats: XML and ASN.1 − 1 gi|730028|sp|P40692|MLH1_HUMAN − DNA mismatch repair protein Mlh1 (MutL protein homolog 1) P − Seq-annot ::= { desc { user { type str "Hist Seqalign", data { { label str "Hist Seqalign", data bool TRUE } } }, user { type str "Blast Type", data { { label id 0, data int 0 } } }, user { type str "BLAST database title", data { { label str "Non-redundant SwissProt Seq-annot ::= { desc { user { type str "Hist Seqalign", data { { label str "Hist Seqalign", data bool TRUE } } }, user { type str "Blast Type", data { { label id 0, data int 0 } } }, user { type str "BLAST database title", data { { label str "Non-redundant SwissProt XML ASN.1

NCBI FieldGuide The Hit Table # BLASTP (Aug ) # Query: gi| |ref|NP_ | MutL protein homolog 1 [Homo sapiens] # Database: swissprot # Fields: query id, subject ids, % identity, % positives, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score # 80 hits found ref|NP_ ||gi| gi| |sp|P38920|MLH1_YEAST e ref|NP_ ||gi| gi| |sp|Q9P7W6|MLH1_SCHPO e ref|NP_ ||gi| gi| |sp|Q8RA70|MUTL_THETN e ref|NP_ ||gi| gi| |sp|Q8KAX3|MUTL_CHLTE e ref|NP_ ||gi| gi|127552|sp|P |MUTL_ECOLI e ref|NP_ ||gi| gi| |sp|Q8FAK9|MUTL_ECOL e ref|NP_ ||gi| gi| |sp|Q8XDN4|MUTL_ECO e ref|NP_ ||gi| gi| |sp|Q72PF7|MUTL_LEPIC e ref|NP_ ||gi| gi| |sp|P57886|MUTL_PASMU e ref|NP_ ||gi| gi| |sp|P44494|MUTL_HAEIN e ref|NP_ ||gi| gi| |sp|Q8ZIW4|MUTL_YERPE e ref|NP_ ||gi| gi| |sp|Q9JYT2|MUTL_NEIMB e ref|NP_ ||gi| gi| |sp|Q9KAC1|MUTL_BACHD e ref|NP_ ||gi| gi| |sp|Q87L05|MUTL_VIBPA e ref|NP_ ||gi| gi| |sp|Q9JTS2|MUTL_NEIMA e ref|NP_ ||gi| gi| |sp|Q6GHD9|MUTL_STAAR e ref|NP_ ||gi| gi| |sp|Q8NWX9|MUTL_STAAW e ref|NP_ ||gi| gi| |sp|Q5HGD5|MUTL_STAAC e ref|NP_ ||gi| gi| |sp|P65492|MUTL_STAAN e ref|NP_ ||gi| gi| |sp|Q9KV13|MUTL_VIBCH e ref|NP_ ||gi| gi|127553|sp|P14161|MUTL_SALTY e ref|NP_ ||gi| gi| |sp|Q9CDL1|MUTL_LACLA e ref|NP_ ||gi| gi| |sp|Q7MH01|MUTL_VIBVY e ref|NP_ ||gi| gi| |sp|Q8Z187|MUTL_SALTI e ref|NP_ ||gi| gi| |sp|Q8DCV0|MUTL_VIBVU e ref|NP_ ||gi| gi| |sp|Q5E2C6|MUTL_VIBF e ref|NP_ ||gi| gi| |sp|Q88DD1|MUTL_PSEPK e Also available in comma separated format for Excel

NCBI FieldGuide PSSMs: Restart PSI-BLAST ASCII encoded, Web only ASN.1 ScoreMat, Portable

NCBI FieldGuide BLAST TreeView Black bear mt genome vs. RefSeq Genomic

NCBI FieldGuide Distance Tree Carnivore Mitochondrial Genome bears walrus fur seal sea lions true seals dogs mongooses cats red panda weasels raccoon

NCBI FieldGuide Genome and Specialized BLAST

NCBI FieldGuide Nucleotide Databases: Human and Mouse Human and mouse genomic and transcript now default Separate sections in output for mRNA and genomic Direct links to Map Viewer for genomic sequences Megablast, blastn service

NCBI FieldGuide Genome BLAST pages

NCBI FieldGuide Map Viewer Homepage

NCBI FieldGuide Poplar Genome BLAST

NCBI FieldGuide tblastn Genome BLAST Results Protein-nucleotide alignments Exons and genes mixed

NCBI FieldGuide Genomic Context of BLAST Hits

NCBI FieldGuide Hits in Map Viewer

NCBI FieldGuide Specialized BLAST Pages

NCBI FieldGuide BLAST URL API

NCBI FieldGuide BLAST: standalone, clients, databases ftp> open ftp.ncbi.nih.gov. ftp> cd blast ftp> open ftp.ncbi.nih.gov. ftp> cd blast

NCBI FieldGuide Standalone BLAST C toolkit BLASTC++ toolkit BLAST BLAST E:\Blast\bin>blastall –i purf.fsa –d swissprot –p blastp BLAST+ E:\blast+\bin>blastp –query purf.fsa –db swissprot BLAST E:\Blast\bin>blastall –i purf.fsa –d swissprot –p blastp BLAST+ E:\blast+\bin>blastp –query purf.fsa –db swissprot

NCBI FieldGuide Service Addresses General Help BLAST Telephone support: