User: madapada

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madapada0
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Posts by madapada

<prev • 6 results • page 1 of 1 • next >
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Answer: A: Domain search tool for aligned+trimmed dataset?
... I heard that CDD might be the tool that I've been looking for. I'll leave this post for anyone who might have similar questions! ...
written 4 weeks ago by madapada0
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Domain search tool for aligned+trimmed dataset?
... Hi. I wonder if there're any tools (regardless of whether it's web-based/or can be downloaded and used via command-line/or GUI) for searching domains from aligned and trimmed protein sequence. I've done that manually via using my eyes (...) and InterPro, but because it took too much time I'm lookin ...
gene alignment written 5 weeks ago by madapada0
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Answer: A: One to one ortholog detection by RBH blast (Reciprocal best hit)
... Also, I have read very good articles from this site about defining ortholog genes. I would recommend these articles for anyone who has similar problems to mine! **What Is The Best Method To Find Orthologous Genes Of A Species?**: https://www.biostars.org/p/7568/ **Inference orthology relationship ...
written 10 weeks ago by madapada0
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One to one ortholog detection by RBH blast (Reciprocal best hit)
... Hello! I'm trying to define one to one ortholog gene sets from various mammals' CDS data from NCBI RefSeq. My goal is to get an ortholog matrix only with one to one ortholog genes, which would be aligned and analyzed by some evolutionary programs to find interesting clade-specific genetic variants. ...
genome cds ortholog rbh blast written 10 weeks ago by madapada0
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Comment: C: If there are two or more B genes with same highest bit score in RBH method
... Hi lieven.sterck. Thanks for your kind explanation! It helps me a lot, especially for understanding the limitation of RBH method and the definition of one-to-one orthologs. But there are still some questions remained. Could you help me some more, please? I couldn't provide my reverse blast results ...
written 10 weeks ago by madapada0
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If there are two or more B genes with same highest bit score in RBH method
... Hi. I want to analyze the coding sequence (CDS) data of closely related vertebrates in NCBI database. Most of the species are in the same order. So I've been looking for the proper method to obtain ortholog gene sets from CDS data of these species and now I try RBH method (Reciprocal best hit) by BL ...
genome sequence written 10 weeks ago by madapada0 • updated 10 weeks ago by lieven.sterck2.6k

Latest awards to madapada

Scholar 4 weeks ago, created an answer that has been accepted. For A: Domain search tool for aligned+trimmed dataset?

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