User: guillaume.rbt

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guillaume.rbt830
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Posts by guillaume.rbt

<prev • 223 results • page 1 of 23 • next >
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Comment: C: Blastp against (only) human Sars-cov1 : which taxid?
... I think I understand, I was using refseq and not nr as database, and it didn't include the bat strains sequences. ...
written 5 months ago by guillaume.rbt830
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Comment: C: Blastp against (only) human Sars-cov1 : which taxid?
... Ok thanks! FYI I tried to blast with a sequence coming from a bat strain, specifyin the 694009 taxid, and I didn't get a perfect match. The best match being a sequence from the human reference. Which lead me to think that sequences from bat strains are not included in the blast search. ...
written 5 months ago by guillaume.rbt830
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Comment: C: Blastp against (only) human Sars-cov1 : which taxid?
... Yes it seems to come from bats, but if I could I would like to focus on human strains. I'm a bit confused by the fact that the taxid is the generic ID for SARS like coronaviruses, which seems to include bat strains (https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=694009). But at the same ...
written 5 months ago by guillaume.rbt830
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Comment: C: Blastp against (only) Sars-cov1 : which taxid?
... Thank for your input. Is 333387 a bat strain? I would like to blast againt a human sars-cov1 strain. ...
written 5 months ago by guillaume.rbt830
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Comment: C: Blastp against (only) Sars-cov1 : which taxid?
... Thank for your help. I've indeed checked this taxid on the taxonomy section of NCBI. It includes sequences from a lot of strains, including Bat coronavirus strains, and I would like to focus on human strains. Even when I exclude sars-cov2 I will still have all the bat strains (if I understand correc ...
written 5 months ago by guillaume.rbt830
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Blastp against (only) human Sars-cov1 : which taxid?
... Hi all, I'm trying to blast peptides against human Sars-cov1 with blastp. I'm not quite sure which taxid I should use to keep only results from Sars-cov1. When I search the term "sars" in the organism field, it proposes "HCoV-SARS (taxid:694009)", but this taxid includes a lot of different coronav ...
blastp written 5 months ago by guillaume.rbt830
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Makeblastdb refseq viral protein sequence (Blast db v5)
... Hi all, I'm trying to create a refseq viral protein sequence blast database. I would like to use the latest (V5) blast db files (https://ftp.ncbi.nlm.nih.gov/blast/db/v5/), to be able to specify taxid in my requests. Would someone know a way to download only viral sequences, or do I have to downloa ...
refseq blast written 5 months ago by guillaume.rbt830
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Answer: A: How to do BLASTP for short sequences (<20 aa) effectively?
... As you mentionned, you have to use the option blastp-short when blasting short sequence. This option will modify several blastp parameters, see here : https://www.ncbi.nlm.nih.gov/books/NBK279684/table/appendices.T.blastp_application_options/ It is explained there that this option should be activa ...
written 5 months ago by guillaume.rbt830
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Comment: C: gene expression correlation positive controls scRNAseq
... I used TCGA to check quickly the correlation between the genes, but I indeed work on scRNAseq. ...
written 5 months ago by guillaume.rbt830
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Comment: C: gene expression correlation positive controls scRNAseq
... thanks ! I've found ABCF1 and ABCF2 that seems to be good candidates (R=0.81 on all TCGA normal samples) ...
written 5 months ago by guillaume.rbt830

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