Forum: Search for gene variants
0
gravatar for Rm
2.3 years ago by
Rm8.0k
Danville, PA
Rm8.0k wrote:

Biologists and clinicians are often faced with searching the literature for a set of given gene variants. There are a number of possible routes they could take, from using specialized databases (odd are they don't know about these) to simply using google. What are the common ways that you search for this kind of information and why do you prefer those ways? how you search for gene variants in google:

for example :

"MSH6" ( rs63750617 | "c.3226C>T" | "c.3226C->T" | "c.3226C-->T" | "c.3226C/T" | "p.Arg1076Cys" | "Arg1076Cys" | "R1076C" )

All possible ways variants are represented for easier searches

next-gen forum • 808 views
ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Rm8.0k
1

I don't. I use dbSNP or EnsEMBL. Not every variant report page is indexed by Google and I'm not interested in every Google-indexed page that mentions the variant.

ADD REPLYlink written 2.3 years ago by _r_am31k

Most of the novel variants are not YET reported in dbSNP or EnsEMBL etc. I believe Google is a good alternative to look for recent reports of publications

ADD REPLYlink written 2.3 years ago by Rm8.0k

pubmed is a good alternative.

ADD REPLYlink written 2.3 years ago by _r_am31k

Pubmed is one of the best options, my intention was to alternate ways we often quickly search for variants reported (maybe by chromosome: position, by transcripts etc...

ADD REPLYlink written 2.3 years ago by Rm8.0k

You might just update your post with that or a variant of what I wrote in a comment. The replies will probably be more useful then :)

ADD REPLYlink written 2.3 years ago by Devon Ryan97k

What's your question/intention of this post?

ADD REPLYlink written 2.3 years ago by finswimmer14k

alternate ways we fellow researchers search for variants

ADD REPLYlink written 2.3 years ago by Rm8.0k

This post is lacking in detail (you are a moderator so you should be setting a good example). What is the link going to? What do you mean by this?

alternate ways we fellow researchers search for variants

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by genomax92k

it's a simple and straightforward: how we search for a variant : "MSH6" ( rs63750617 | "c.3226C>T" | "c.3226C->T" | "c.3226C-->T" | "c.3226C/T" | "p.Arg1076Cys" | "Arg1076Cys" | "R1076C" ) is the query and link will take you to the result in google (google is just one way). Where we can look for latest literature reporting the same, apart from that specialized DBs

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Rm8.0k

Google is not great at searching journal articles, the least you'd need to do is switch to Google Scholar. Pubmed is better and has a lot more pertinent filters.

ADD REPLYlink written 2.3 years ago by _r_am31k

Can the post essentially be rephrased as the following?

Biologists and clinicians are often faced with searching the literature for a set of given gene variants. There are a number of possible routes they could take, from using specialized databases (odd are they don't know about these) to simply using google. What are the common ways that you search for this kind of information and why do you prefer those ways?

If that's not more or less what you're going after then please clarify :)

ADD REPLYlink written 2.3 years ago by Devon Ryan97k

Well said @DevonRyan

ADD REPLYlink written 2.3 years ago by Rm8.0k

search by dbSNP ID (first field within brackets) in dbSNP. That would get you rest of the HGVS notations you have posted or probe ENSEMBL API with rsIDs to fetch HGVS syntax for variants @ Rm

ADD REPLYlink written 2.3 years ago by cpad011214k
2
gravatar for jared.andrews07
2.3 years ago by
jared.andrews077.9k
Memphis, TN
jared.andrews077.9k wrote:

Probably the most comprehensive programmatic option I know is the MyVariant.info API, which is very easy to use in python, R, or javascript.

Queries can be gene symbols, chromosome positions, variant IDs, etc.

There is a kind of half-baked but fully-functional web interface somebody made for it here as well.

ADD COMMENTlink written 2.3 years ago by jared.andrews077.9k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1971 users visited in the last hour