DATA ACQUISITION FROM BIO-DATABASES AND BLAST. Natapol Pornputtapong 18 January 2018
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1 DATA ACQUISITION FROM BIO-DATABASES AND BLAST Natapol Pornputtapong 18 January 2018
2 DATABASE Collections of data To share multi-user interface To prevent data loss To make sure to get the right things Bioinformatics for Phylogenetic Analysis Workshop 2
3 LIBRARY -> DIGITAL LIBRARY Bioinformatics for Phylogenetic Analysis Workshop 3
4 DATABASE: A LIBRARY OF DATA Database Files, Tables, Records Data structure Database management system Programming interface User interface Library Books building, shelves Librarian Protocols, SOPs Services Bioinformatics for Phylogenetic Analysis Workshop 4
5 ADVANTAGE OF DATABASE Data integrity Smaller space Data availability Speed Bioinformatics for Phylogenetic Analysis Workshop 5
6 DATABASE FOR USERS Search Database Download Users Submission Bioinformatics for Phylogenetic Analysis Workshop 6
7 HOW TO CHOOSE DATABASE? 1695 bio-databases in NAR online Molecular Biology Database Collection in 15 categories Bioinformatics for Phylogenetic Analysis Workshop 7
8 DATA CONTENT Literature DNA sequence GenBank Protein sequence RefSeq TrEMBL Bioinformatics for Phylogenetic Analysis Workshop 8
9 CONCEPTS OF DATABASE Primary database Secondary database interface interface Database Database Database Database Database Source Source Source Bioinformatics for Phylogenetic Analysis Workshop 9
10 PRIMARY & SECONDARY DB Primary database Secondary database Synonyms Archival database Curated database; knowledgebase Source of data Examples Direct submission of experimentally-derived data from researchers ENA, GenBank and DDBJ (nucleoti de sequence) ArrayExpress Archive and GEO (functional genomics data) Protein Data Bank (PDB; coordinates of three-dimensional macromolecular structures) Results of analysis, literature research and interpretation, often of data in primary databases InterPro (protein families, motifs and domains) UniProt Knowledgebase (sequence and functional information on proteins) Ensembl (variation, function, regulation and more layered onto whole genome sequences) Bioinformatics for Phylogenetic Analysis Workshop 10
11 DATA COLLECTION CRITERIA GenBank RefSeq GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences Bioinformatics for Phylogenetic Analysis Workshop 11
12 Bioinformatics for Phylogenetic Analysis Workshop 12
13 ACCESSIBILITY: TOOLS & INTERFACES NCBI Entrez RESTful interface to the ENA Bioinformatics for Phylogenetic Analysis Workshop 13
14 NCBI SEARCH TOOL Bioinformatics for Phylogenetic Analysis Workshop 14
15 SIMPLE SEARCH Bioinformatics for Phylogenetic Analysis Workshop 15
16 BOOLEAN OPERATOR Bioinformatics for Phylogenetic Analysis Workshop 16
17 FILTER Limit with filter Advanced search builder Bioinformatics for Phylogenetic Analysis Workshop 17
18 RESULTS Bioinformatics for Phylogenetic Analysis Workshop 18
19 BLAST: BASIC LOCAL ALIGNMENT SEARCH TOOL Bioinformatics for Phylogenetic Analysis Workshop 19
20 MAJOR BLAST PROGRAMS Bioinformatics for Phylogenetic Analysis Workshop 20
21 BLAST SEARCH Bioinformatics for Phylogenetic Analysis Workshop 21
22 Bioinformatics for Phylogenetic Analysis Workshop 22
23 OTHER BLAST PROGRAMS Bioinformatics for Phylogenetic Analysis Workshop 23
24 WORLD OF FILES Text files Binary files Bioinformatics for Phylogenetic Analysis Workshop 24
25 TEXT FILES: WORLD OF FORMATS MS Words:.doc,.docx,.rtf,.txt Sequence: FastA (.fasta), Genbank (.gbk) Protein structure: PDB (.pdb) Bioinformatics for Phylogenetic Analysis Workshop 25
26 FASTA FORMAT >P01013 GENE X PROTEIN (OVALBUMIN-RELATED) QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMP FHVTKQESKPVQMMCMNNSFNVATLPAEKMKILELPFASGDL SMLVLLPDEVSDLERIEKTINFEKLTEWTNPNTMEKRRVKVY LPQMKIEEKYNLTSVLMALGMTDLFIPSANLTGISSAESLKI SQAVHGAFMELSEDGIEMAGSTGVIEDIKHSPESEQFRADHP FLFLIKHNPTNTIVYFGRYWSP > Bioinformatics for Phylogenetic Analysis Workshop 26
27 GENBANK FORMAT Bioinformatics for Phylogenetic Analysis Workshop 27
28 NEXUS FORMAT #NEXUS BEGIN DATA; DIMENSIONS NTAX=8 NCHAR=1202; FORMAT MISSING=? DATATYPE=PROTEIN GAP=-; OPTIONS GAPMODE=MISSING; MATRIX [ ] [ ] Homo_sapiens_ TERLVLPPPDPLDLPLRAVEL... Pan_troglodytes_ TERLVLPPPDPLDLPLRAVEL... Ailuropoda_melanoleuca_ TERLVLPPPDPLDLPLRPVEL... Mus_musculus_ TERLVLPPLDPLNLPLRALEV... Danio_rerio_ MDKIDLPPVGPDDLPLSLLEM... Xenopus_tropicalis_ MNTLDLSNRDPLDLPLSVLEL... Monodelphis_domestica_ TERLVLPPRGPLDLPLCALEL... Canis_familiaris_ TERLALPPPDPLDLPLRPVEL...; END; Bioinformatics for Phylogenetic Analysis Workshop 28
29 NEXT Inputs Analysis Results Bioinformatics for Phylogenetic Analysis Workshop 29
30 QUESTION? Bioinformatics for Phylogenetic Analysis Workshop 30
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