Human Genome Browser

1
???-??????????????? ???? ?????? ? ????????
????????

• ??? ????? ???-??????????????? ???? ???????
• ????? ??????? ??????? ????? ??
• ??????? ?????-??????????????? ??? ?????? ?
  ???????? ????????
• Human Genome Browser

2
??? ????? ???-??????????????? ???? ???????

• ??????? ???????????? ??? (? ??
  ????????????????? ??????????????????)
• ???????? ???????? ??????????? ?? ???????????
  ????, ? ?? ???????????????????, ??????????? ??
  ??????? ??????????? ???? ??????????? ??? ?????
  ????? ? ?????? ????? ?? ???

3
?????? ?????? Gene Entrez (?????? LocusLink) ?
NCBI

• ??????? ???????????? ????? ?????????? ?????
  ?? ?????????, ?????????? ?????? ????? ?/???
  ??????????????? ??????? ????

4
DUT ??? ????????
5
??????????? ??????

• Bibliography
• Related Articles in PubMed
• GeneRIFs Gene References Into Function
• Interactions
• General gene information
• Markers
• Genotypes
• Pathways
• Homology
• GeneOntology
• General protein information (Names, ECs, ACs)
• NCBI Reference Sequences (RefSeq)
• mRNAs and proteins
• Reference assembly Alternate assembly Genomic
• Related Sequences (links between ACs of different
  types)
• Additional Links (OMIM, PharmGKB, HRDP, UniGene)

6
MapViewer
7
???????? ???? ??????

• ?????? ?????? ?????
• ??????????? ???????????? ??????? ??? ???? ??????
  ??????
• ????????? ???? ? ?????? ????? ???????
  ????????????? ???????? (comparative genomics)
• ?????????? ???? ????????? ?????????? ? ??????
  ??????
• ???????? ?????????? ? ?????, ?? ? ????????
  ?????????
• ???????? ???????? ??????????? ?????????????
  ???? ??????????????? ??????????
• NCBI -gt Genomic Biology (http//www.ncbi.nlm.nih.g
  ov/Genomes/)

8
???????? ??????
??? ???????? ????? (?????? ???????? ?????? ???
?????? ??????? ?????? ??????????)
http//www.ncbi.nlm.nih.gov/genomes/VIRUSES/viruse
s.html
9
HIV2 ?????
10
Sequence Viewer
11
Protein coding genes link
12
gMap (comparative genomics)

• Zoom in, zoom-out
• ??????? ???????????? ???????
• ??? ???????
• (!) ??????????? ????? ? ?????? ???? ????!

13
????????????? ?????? ?? ????? NCBI
Tools legend T - TaxMap P - ProtTable C - COG
Table D - 3-D neighbors L - BLAST S - CDD
search G - GenePlot X - TaxPlot M - gMap F -
FTP R - Publications
14
COG Table
15
COG Table ?????? (Overview)
16
TaxMap

• ?????? ????? ???
• ????????? ????? ???????, ????? ????
• ???? ????????????? ??????? ??????? BLAST-????
• ?????? ???? ????????????? ??????
• ????????????? ???? ????? ????? ?????? ?????????
• Click ?? ????? ?????? ????? ????? ? ????????

17
Genomes in progress
18
TIGR Comprehensive Microbial Resources
http//cmr.tigr.org/tigr-scripts/CMR/CmrHomePage.c
gi
????????? ?? ???????????, ? ?? ?? ??????
19
??? ?????? ?? TIGR
20
?????????

• NCBI Map Viewer, FTP ??? ??????
  ??????????????????, ??????????????? ??????,
  ?????? ?? ?????????????????? ???? ??????
• MapViewer ??????? LocusLink

21
Human

• ??? ???????? ????????
• Ensembl (http//www.ensembl.org) EBI Sanger
  Institute, ?????????? ???? IDs, 35
  ??????????????? ?????
• Human Genome Browser (http//genome.ucsc.edu
  /) UCSC, USA
• ?????????? GenBank IDs, 41 ??????????????? ???

22
Ensembl
Ensembl Tutorials and Worked Examples
http//www.ensembl.org/info/helpdesk/tutorials/in
dex.html
23
Human Genome Browser
RefSeq ID Chr Band Gene name Coords
24
DUT gene (dUTPAse)
25
?????? RefSeq ?????
26
Provided tracks (types)
27
Custom Track

• ??????????? ??????????????? ???? ???????????
  ????????? ????? ??????????? ?????-???? ?????
  ???????
• Upload ? BED, GFF, GTF, WIG ??? PSL ???????
• ????.,
• chr1 15003 19498 name1 1
• chr1 58954 59871 name2 1
• chr1 321669 332669 name3 1 -

28
??? ??? ?????????
29
BLAT

• BLAT BLAST ? ???????????, ????????????????? ??
  ????? ??????????? ???????????????-???? ? ??????
  ??????

30
Table Browser