Bioinformatics On Genomics

Hsueh-Fen Yuki Juan

April 28, 2003

Outline Gene Sequence Searching Cutting Site for a Specific Sequence Sequence Alignment Search for Conserved Domains ORF Finding

Gene Sequence Searching Cutting Site for a Specific Sequence Sequence Alignment Search for Conserved Domains ORF Finding

Accession Number

Gene Sequence

Gene Sequence Searching

http://www.ncbi.nlm.nih.gov/UniGene/

AA046701AA069414AA070289AA446013AA425102

GGGGGGGGGAAGCTGAGCGCTGAGACCAAGGGCTAAAGCTGGGAGACTGAAAAAATGCAGACCGCCGGGGCATTATTCATTTCTCCAGCTCTGATCCGCTGTTGTACCAGGGGTCTAATCAGGCCTGTGTCTGCCTCCTTCTTGAATAGCCCAGTGAATTCATCTAAACAGCCTTCCTACAGCAACTTCCCACTCCAGGTGGCCAGACGGGAGTTCCAGACCAGTGTTGTCTCCCGGGACATTGACACAGCAGCCAAGTTTATTGGTGCTGGGGCAGCCACAGTTGGTGTGGCTGGTTCAGGGGCTGGCATTGGAACCGTGTTTGGCAGCTTGATCATTGGCTATGCCAGGAACCCGTCTCTCAAGCAGCAGCTCTTCTCCTATGCCATTCTTGGCTTTGCCCTGTCTGAGGCCATGGGGCTTTTCTGTTTGATGGTCGCCTTCCTCATCCTCTTCGCCATGTGAGGCTCCATGGGGGGTCACCGGCCTGTTGCTACTGCAACTCCACACCATTCTTGGTGCTGGGGTGTGTTAAGCTTTACCATTAAACACAACGTTTCTCTAAAAAAAAAAAAAAAAAAAAC

Gene Sequence Searching Cutting Site for a Specific Sequence Sequence Alignment Search for Conserved Domains ORF Finding

Cutting Site for a Specific SequenceSequence

Cut by Restriction Enzymes1. RestrictionMapper2. REBASE3. NEBcutter4. DARWIN

RestrictionMapperhttp://www.restrictionmapper.org

REBASERebase.neb.com/rebase.html

DARWINhttp://darwin.bio.geneseo.edu/~yin/WebGene/RE.html

Gene Sequence Searching Cutting Site for a Specific Sequence Sequence Alignment Search for Conserved Domains ORF Finding Primary Structure Analysis: Amino a

cid composition, pI and MW Protein Sequence Searching Proteomics Tools

Input Query

Amino Acid Sequence DNA Sequence

Blastp tblastn blastn blastx tblastx

Compares Against protein Sequence Database

Compares Against Translated Nucleotide Sequence Database

Compares Against Nucleotide Sequence Database

Compares Against protein Sequence Database

Compares Against Translated Nucleotide Sequence Database

Sequence Alignment

http://www.ncbi.nlm.nih.gov/

BLAST

Copy Sequence

Pairwise BLAST

Gene Sequence Searching Cutting Site for a Specific Sequence Sequence Alignment Search for Conserved Domains ORF Finding

Search for Conserved Domains

Gene Sequence Searching Cutting Site for a Specific Sequence Sequence Alignment Search for Conserved Domains ORF Finding

ORF Finder (Open Reading Frame Finder)http://www.ncbi.nlm.nih.gov/gorf/

Useful Bio-WebsiteseuGene

http://iubio.bio.indiana.edu:8089/

Proteome Analysis @EBI

http://www.ebi.ac.uk/proteome/

GeneCards

http://genecards.ym.edu.tw/