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Old 01-26-2011, 07:33 AM   #1
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Location: Germany

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Default Annotation tools for NGS data


my name is Frank Schacherer. I work for a bioinformatics company called BIOBASE (, which creates biological databases.

We recently launched a tool to screen ngs variation data, called Genome Trax (see it life here: http://custom.biobase-international....ometrax-chr21/). The tool contains annotation like mutations and binding sites for transcription factors mapped to genome coordinates. You can use it to find if some variants you detected are already known to have a functional impact, or fall in a region that makes this probable.

I would like to invite you to try out the free version of the tool, or get in touch with me if you are interested in accessing the full version for your research. My hope is that we can make the tool more useful for everyone.

Some background about the data included: We manually collect research findings, and organize them neatly in easy-to-search in biological databases. Two of the better known of these databases are TRANSFAC, which collects transcription factor binding sites, and HGMD, which contains all known disease-causing mutations, and disease-related polymorphisms. We also have a database called PROTEOME with functional characteristics for genes and proteins, like diseases, and drug relationships, pathways, and posttranslational modifications.

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Old 01-26-2011, 08:51 AM   #2
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Join Date: Apr 2010
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Hi Frank,
This could be very useful tool for exom/whole genome analysis pipeline, I am interested to try it on an exom sample. We already have copy of HGMD Pro and I was thinking about getting Genome Trax but I have a question after looking at the comparison chart shows that Genome Trax 2010.3 has less information that whats included in HGMD Professional specifically the Mutations associated with inheritable human disease 80,700+ vs HGMD Pro 105,000+. Also SNPs 31,427 vs 60,489 (disease-linked) in HGMD Pro. Why isn't Genome Trax inclusive of everything in HGMD Pro? is it going to be in future releases?

p.s. referring to

Last edited by husamia; 01-26-2011 at 08:53 AM.
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Old 01-26-2011, 09:45 AM   #3
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"Why isn't Genome Trax inclusive of everything in HGMD Pro? is it going to be in future releases?"

The reason for this difference is that not all of the mutations in HGMD Pro have been mapped to exact genomic coordinates yet.

In some cases, it is not easy to do this mapping without going back to the original paper (for example, take mutation CP065938, where the description of the mutation reads: "Del. 1049 bp incl. ex.3, ins 7"), and sometimes if the mutation is described to vaguely, it can not be mapped exactly at all.

In other cases, like for small indels, it is possible, but it still requires manual review, when the site of mutation is given relative to some other feature or in descriptive terms, to verify it is being mapped to the right coordinates.

We are in an ongoing effort to map everything in HGMD Pro that can possibly be mapped to coordinates, and are extending the percentage of coordinate-mapped mutations with each release. While I do not believe it will be possible to resolve this for 100% of the mutations, the percentage of HGMD Pro mutations in future releases is going to increase accordingly.

This also means that for purposes of using data from HGMD Pro to analyze whole genome variations, you would not without a lot of effort be able to get more out of HGMD Pro than out of Genome Trax. That's why we provide, GenomeTrax, so we have this effort, not you :-)

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Old 01-26-2011, 11:24 PM   #4
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Moved to the vendor forum. Please start threads related to commercial products there.
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