Department of Cell Biology

B. Hilda Ye, PhD -- Bioinformatics


Associate Professor
Department of Cell Biology
Chanin Bldg., Room 302C

Research Interest
Lab Members
Online Journals
Lymphoma Links
Online Books & Science Portals



Information on a Gene 


OMIM  Online Mendelian Inheritance in Man
The Gene Card  Integrate all biomedical information on a gene

Sequence Retrieve 


NCBI Tool Page  BLAST, Orthologous, human-mouse homology, Map Viewer, LocusLink, Vast Search, The Cancer Chromosome Aberration Project, The Cancer Genome Anatomy Project, and lot more!
ENTREZ  Retieve DNA or Protein sequence from GenBank

Database Search 


BLAST Similary Search  Remember to search NR, EST and STS to get complete coverage
Mouse Genome Database  1.The 2000–2001 Mouse Chromosome Committee Reports 2. Release 15 of the MIT microsatellite map (Oct 1997) 3. The recombinant inbred strain database of R.W. Elliott (1997) and R. W. Williams (2001) 4. Map Manger and text format chromosome maps (Apr 2001)
Human and mouse genome at UC Santa Cruz  Assembled human and mouse genome by the public consortium. Very quick result and Nice browser function with the Blat search.
BLAST C. Elegan  Complet C. Elegan Genome
BLAST Yeast  Complet Yeast Genome
TIGR Zebrafish Genome Blast 
ZFIN Zebrafish Genome Database Project 
Genomatix  Genomatix Home
Database of transcription start sites  Precise 5' end of cDNA sequences based upon the “oligo-capping” method. By Feb 2002, contains 7889 human genes, 59% of them have extended 5’ termini compared to the NCBI sequences.)



GeneMap99  Search by position or maker name. Unfortunately, you can't search the database by sequence.
UniGene  Search by position or maker name. Unfortunately, you can't search the database by sequence.
BAC/PAC Resource  Standard human and mouse BAC, PAC libraries (Complete Coverage)

Gene Identification 


GenScan  Intron-Exon boundaris. Good for medium size of genomic DNA sequence
WebGene  Tools for prediction and analysis of protein-coding gene structure in Italy



The RNA World  A good resource for RNA related stuff. Web site is slow.



ScanProsite  analysis of protein sequences, MW, PI, structures, as well as 2-D PAGE
ProfileScan Server  Motif Scan in a Protein Sequence
Codon Usage  Search by Latin names of the organism
GOR IV  Secondary structure
TMHMM  Prediction of transmembrane helices in protein orientation at EMBnet-CH



The Jackson Laboratory  Mouse Geome Informatics
The Whole mouse catalog  everything about mouse research
KO mice with immunophenotype (Jackson)  Also, link to tumor biology, gene expression, and mouse genome database etc.

Cell Culture 


ATCC  Cell line, DNA etc. collection

Last Update: Friday, January 30, 2009 

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