One Gene, Many Sequences.ppt

1、Getting More From Your Malaria Molecular Data on the Web:,Chuong Huynh National Center for Biotechnology Information, National Library of Medicine, National Institute of Health,A Survey of PlasmoDB, MGP, NCBI Resources,Homology,. Is the central concept of all biology. Whenever we say that a mammalia

2、n hormone is the same hormone as a fish hormone, that a human gene sequence is the same as a sequence in a chimp or a mouse, that a HOX gene is the same in a mouse, a fruit fly, a frog, a human even when we argue that discoveries about a worm, a fruit fly, a frog, a mouse, or a chimp have relevance

3、to the human condition we have made a bold and direct statement about homology. The aggressive confidence of a modern biomedical science implies that we know what we are talking about.” - David B. Wake,The Big Picture Concept,Comparative analysis in biology -e.g. Leishmania and Plasmodium Genotype t

4、o Phenotype, Protein sequence MKIVYWSGTGNTEKMAELIAKGIIESGKDVNTINVSDVNI DELLNEDILILGCSAMGDEVLEESEFEPFIEEISTKISGK KVALFGSYGWGDGKWMRDFEERMNGYGCVVVETPLIVQNE PDEAEQDCIEFGKKIANI, DNA sequence AATTCATGAAAATCGTATACTGGTCTGGTACCGGCAACAC TGAGAAAATGGCAGAGCTCATCGCTAAAGGTATCATCGAA TCTGGTAAAGACGTCAACACCATCAACGTGTC

5、TGACGTTA ACATCGATGAACTGCTGAACGAAGATATCCTGATCCTGGG TTGCTCTGCCATGGGCGATGAAGTTCTCGAGGAAAGCGAA TTTGAACCGTTCATCGAAGAGATCTCTACCAAAATCTCTG GTAAGAAGGTTGCGCTGTTCGGTTCTTACGGTTGGGGCGA CGGTAAGTGGATGCGTGACTTCGAAGAACGTATGAACGGC TACGGTTGCGTTGTTGTTGAGACCCCGCTGATCGTTCAGA ACGAGCCGGACGAAGCTGAGCAGGACTGCATCGAATTTGG TAAG

6、AAGATCGCGAACATCTAGTAGA,The Big Picture Concept,Colon cancer gene sequence,Human 638 RHACVEVQDEIAFIPNDVYFEKDKQMFHIITGPNMGGKSTYIRQTGVIVLMAQIGCFVPC 697 Yeast 657 RHPVLEMQDDISFISNDVTLESGKGDFLIITGPNMGGKSTYIRQVGVISLMAQIGCFVPC 716 E.coli 584 RHPVVEQVLNEPFIANPLNLSPQRR-MLIITGPNMGGKSTYMRQTALIALMAYIGSYVPA 642,

7、Homology implies a common ancestry which may be inferred from observations of sequence similarity,The Big Plan,1: Human Genome Resources,Information on: * Genes - LocusLink 5582 EST P. falciparum: 1726 GSS; 1117 EST P. vivax: 10545 GSS Are there any novel genes represented in the EST database that a

8、re related to this known gene or family of genes or contains this known protein domain? Are there any ESTs similar to my sequence? - sequence search (Use NCBI CustomBlast; Pre-clustered EST search, e.g. Unigene) Are there any ESTs derived from a gene encoding a protein that contains my domain? - mot

9、if search (CDD; Pfam)7,/,Jane Carlton,John Dame,3. Mosquito Genomics WWW Server / AnoDB,Mark Benedict,Other Useful NCBI Resources,Entrez Retrieval System - LocusLink - RefSeq - UniGene -,Entrez Retrieval System,Entrez is a retrieval system for searching several linked da

10、tabases with precomputed similarity searches (neighbors) for many of the databases.,What does this mean?,You are able to move effortlessly from a full text published literature to DNA sequences to the proteins they encode to chromosome maps of the genes and to the 3-D structures of the proteins. Get

11、ting the specific information that you want in a comprehensible manner.,LocusLink and RefSeq,/LocusLink/,LocusLink: Catalog of named human, mouse, rat, fruit fly, zebra fish loci with stable locus IDs and many cross-references. Gene-centric. Malaria (PlasmoDB) and mosquitoe

12、s,RefSeq: Reference mRNA sequence for each locus,RefSeq: NCBI Reference Sequence Project,Supplement gene products with useful sequence analysis information such as a list of best hits in different taxa, predicted functions in uncharacterized gene products, frame shifted proteins, and more.,LocusLink,/LocusLink/,Information on: phenotypes, nomenclature, gene maps, reference sequences, and related resources: PubMed citations, Omim, RefSeq, GenBank, UniGene, and dbSNP(V) records,Using LocusLink,GeneRIF (Gene References into Fun