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Bioinformatics Algorithms Research - Message forums

Discussion forums: Open Discussion

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Welcome to Open Discussion
Submitted by Unset; posted on Thursday, June 12, 2003
Welcome to Open Discussion
BLAST
Submitted by Nobody; posted on Thursday, August 21, 2003
Hello; Does anyone have any statistical data on: 1. the number of web sites world-wide providing BLAST or BLAST-like searches? 2. The number of bioinformaticists in the US and rest of world? 3. No of people using such search services? NCBI BLAST gest about 100,000 search requests/day. How many users does this represent on average? 4. Geographical distribution of bioinformaticists (US, Europe, UK, Japan, Canada, Australia, China, India, others?)? 5. Do any sites charge for searches? 6. How many algorithms have been written for local sequence alignment? Thanks Damon
visualization of large sequences or genomes
Submitted by dengxuegong; posted on Thursday, October 13, 2005
We present a technique for the visualization of large sequences or genomes. We use fractal theory to express DNA sequence as a Hilbert-Peano curve which transforms the sequence to a two dimensional image. This image can then be subjected to standard image processing techniques to reveal characteristic structures of interest that exist in the sequence. We have applied the technique to a number of well annotated genomes to demonstrate that the observed structures in the curves correspond to real features. We have also analyzed the less well annotated chicken and zebrafish genomes to identify distinctive characteristics in both species that have not been identified using existing analysis tools. The method is a useful technique for rapid characterization of genome scale sequences that, when used in concert with existing sequence analysis tools can aid the researcher in the identification of novel features in a genome or large sequence. Finished & unpublished papers 1. Visualization and Analysis of Genome Scale Sequences using Hilbert-Peano Curves 2. Symmetry Phenomena in complete Genomes If you( people , group, institution) are interested in my current work, please mail me at dengxuegong@tom.com
Seeking collaborator in zebrafish genome (transposon)
Submitted by XG Deng; posted on Saturday, April 21, 2007
we found a multcopy repeat sequence in zebrafish genome (ll chromosomes), by our new method DHPC. We suspected that they are a new transposon, this idea is vertifiedby EST blast. but we are not biologists, we hope to cooperate with biologists in this work. who is interested in this work can cantact us by emial dengxuegong@tom.com
Re: Seeking collaborator in zebrafish genome (transposon)
Submitted by XG Deng; posted on Saturday, April 21, 2007
i can open our repeat sequence if one isinterested in cooperation.
rewrite: Seeking collaborator in zebrafish genome (transposon)
Submitted by XG Deng; posted on Saturday, April 21, 2007
we found a multi-copy repeat sequence in zebrafish genome (all chromosomes), by our new method DHPC. We suspected that they are a new transposon, this idea is vertifiedby EST blast. but we are not biologists, we hope to cooperate with biologists in this work. who is interested in this work can cantact us by emial
Seeking collaborator in zebrafish genome (transposon)
Submitted by XG Deng; posted on Wednesday, April 25, 2007
we found a multi-copy repeat sequence in zebrafish genome (all chromosomes), by our new method DHPC. We suspected that they are a new transposon, this idea is vertifiedby EST blast. but we are not biologists, we hope to cooperate with biologists in this work. who is interested in this work can cantact us by email dengxuegong@tom.com any one who isfamiliar with this problem can give me some suggestions? the repeat sequence (2kb) has about 1000 copies. not found any copy in other fish or animal, even though low similar level. if one know who is the expert in this problem tell me please. thanks !
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