First Genome drafts based the Human-Mouse conserved Synteny Regions/Genes/Alignments

webmaster at softberry.com webmaster at softberry.com
Mon Apr 8 05:39:55 EST 2002


Human-Mouse Homology chromosome regions and genes

First Genome drafts based the Human-Mouse conserved Synteny 
Regions/Genes/Alignments

Softberry Inc. developed Human-Mouse Synteny server which provide information 
about 18915 Human genes mapped to Mouse genome draft and 18464 Mouse genes 
mapped to Human genome draft (among them 14504 ortologous gene pairs).

This is the most comprehensive data about Homology between Human and Mouse 
genomic Regions comparing with NCBI homology maps, which contain significantly 
less genes and often do not connect directly with draft genomic sequences Human 
and Mouse. The data was received by proprietary Softberry programs for gene 
prediction, est/RNA mapping and gemomic sequence comparison (some you can test 
on line at www.softberry.com).

   http://www.softberry.ru/berry.phtml?topic=human-mouse


Genes included in this annotation are from three groups: (m) having known mRNA 
from Refseq database, (h) predicted and supported by protein homolog from NR 
database, and (a) ab initio predicted.
All these genes (Fgenesh++ gene sets) are presented in the UCSC Genome Browser 
(Human and Mouse, respectively): http://genome.cse.ucsc.edu/index.html and in 
Genome Explorer Java Browsers at Softberry Inc. servers: Human: 
http://www.softberry.com/berry.phtml?topic=genomexp Mouse: http://p69-
55.acedsl.com:8080/genomexp.html

The server http://www.softberry.ru/berry.phtml?topic=human-mouse

(or http://www.softberry.ru/berry.phtml?topic=human-mouse)

provides a list of Synteny Regions for each (Human/Mouse) chromosome when you 
click on chromosome number (Y chromosome of mouse is absent in draft) and 
coordinates of each region on Human (December01 release) and Mouse (November01 
release) draft sequences.

For each syntenic region you can click on Genes link and see what orthologous 
genes are found in it (some genes in these regions might have no corresponding 
pair known.
It is a good hint that ABSENT mouse/human gene is their, but due to incomplete 
and imperfect genome sequence (especially for MOUSE) it is currently do not 
mapped/known in genome.

You can GET ALIGNMENT on line by clicking [A] link or ALIGNMENT with 
Visualization [AV] (produced instantly by Softberry SCAN2 genomic alignment 
tool http://www.softberry.ru/berry.phtml?topic=scanh&prg=SCAN2 ). In DBSCAN 
JAVA viewer you can PUSH left mous button AND DRAG MOUSE around any part of 
BLOCKS in the top panel and you will see the ALIGNMENT in the middle viewer 
panel.

Remember that usually longer alignment blocks (> 80 bp) corresponding to coding 
exons (with similarity 85-95%) and there are a lot of short similar block 
between them often corresponding to short simple sequences.

You can see genes coordinates and their short descriptions by clicking Genes 
link for each syntenic region (more info about genes see in mentioned above 
Genome Browsers), which will be linked directly with genes shown in syntenic 
regions (in the future).

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