090302_L2.ppt

Lect2. 生物信息的检索 凌毅 Bioinfo_cau@ Previous Lecture What is Bioinformatics Interdisiplineary research area Applied informatics techniques to understand and organize biological information, in a large scale. Considered as computational molecular biology, differ from computational biology Bioinformatics research scope Development / application of computational tools and databases Tools and databases are used in sequence, structural and functional analysis, details are in the figure of 1st lecture ppt, p15. Bioinformatics research limitation Keep in mind! Avoid over-reliance or an over-expectation of bioinformatics output. Major biological databases / websites Database: GenBank, EMBL, DDBJ, PDB, SWISS-PROT, TrEMBL, UniProtKB…(primary, secondary, specialized) Websites: NCBI, EBI, ExPaSy, CBI How to find suitable biological resources for research? From textbook, out links on major bioinformatics websites, key words in search engine, NAR database/Web server issue Previous Lecture II Mainly sequence database: Nucleotides Sequences: EMBL (EBI), GenBank (NCBI), DDBJ (NIG) Protein Sequences: PIR-PSD (stop update), UniProtKB (SwissProt/TrEMBL),  RefSeq, NCBI protein database Importance of accuracy of nucleotide sequence entry Indicated coding sequence on the nucleic acid record Avoid incorrect information in the coding feature of a DDBJ/EMBL/GenBank record Put the information into the appropriate place within a sequence record Sequence format in database FASTA format Begin with a “”, then the description on the lst line; Sequence begin at the 2nd line Database flatfile format: (GenBank/DDBJ, nearly identical; EMBL) Header Feature table: the Source feature must be present on all DDBJ/EMBL/GenBank entries. Sequence Terms EST、 cDNA、 ORF、 UTR、CDS、exon、intron、promoter BAC, YAC GSS、 STS、 SNP Outline for today Other databases contents in NCBI Literature: PubMed, OMIM Molecular Gene: UniGene, Entrez Gene Data submissions Nucleotide sequences: BankIt / Sequin Tools in NCBI