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NCBI-Hackathons / seqr

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Query Parameters #42

Open averagehat opened 9 years ago

averagehat commented 9 years ago

I remember some discussion of default query parameters we should use for querying. I remember there was one in particular that was almost required for Seqr but that information seems to be lost. I want to make sure results/sensitivity are correct to compare with blastx.

lianyi commented 9 years ago

Right, we'd need to fill that in. What's the current parameter being used ( I don't have a computer to access until later today ) ?

Simply & DRY

-----Original Message----- From: Mike Panciera [notifications@github.commailto:notifications@github.com] Sent: Monday, September 14, 2015 12:50 PM Eastern Standard Time To: NCBI-Hackathons/seqr Subject: [seqr] Query Parameters (#42)

I remember some discussion of default query parameters we should use for querying. I remember there was one in particular that was almost required for Seqr but that information seems to be lost. I want to make sure results/sensitivity are correct to compare with blastx.

— Reply to this email directly or view it on GitHubhttps://github.com/NCBI-Hackathons/seqr/issues/42.

averagehat commented 9 years ago

Right now it's just "sequence:" and nothing else

lianyi commented 9 years ago

Perhaps we can add mm ( minimum should match) = 50% for now . The smaller value will include more distant homologous but possible more false positives.

We can also add another flavor : tanimoto score ( will send in another update on this soon), that might better rank the hits.

Simply & DRY

-----Original Message----- From: Mike Panciera [notifications@github.commailto:notifications@github.com] Sent: Monday, September 14, 2015 02:23 PM Eastern Standard Time To: NCBI-Hackathons/seqr Cc: Han, Lianyi (NIH/NLM/NCBI) [C] Subject: Re: [seqr] Query Parameters (#42)

Right now it's just "sequence:" and nothing else

— Reply to this email directly or view it on GitHubhttps://github.com/NCBI-Hackathons/seqr/issues/42#issuecomment-140166164.