Answers.Body: <p>It sounds like your easiest option is to just install blast on your local machine and set up the databases there. It really will only take a few minutes to blast 6,000 sentences against a yeast genome on a modern laptop. Any solution interfacing with web results or parsing the output will be painfully convoluted. There are executables for blast that will work on Mac, Linux, or Windows.</p>
  
  <p>Some beginning instructions for installing it on your laptop can be found here: <a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastDocs&amp;DOC_TYPE=Download" rel="noreferrer">https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastDocs&amp;DOC_TYPE=Download</a> . Make sure to pass the --num_threads option to speed up the search. </p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-12-24T06:00:11.337Z
Answers.LastActivityDate: 2018-12-24T06:00:11.337Z
Answers.UserDisplayName: conchoecia
Body: <h3>Context</h3>
  
  <p>I'm an MSc student working on writing up my thesis (back home now) from my laptop and, therefore, unfortunately don't have access to a workstation/server capable of doing the tBLASTn search that I wanted to do. As a result I have been trying to use as many online resources as possible. </p>
  
  <h3>Question</h3>
  
  <p>Is there a way to export the tBLASTn results from the NCBI website to a simple text file? I want the output to be something similar to:</p>
  
  <pre><code>FASTA_Name Max_score Total_score Query_cover E_value Identity Accession Gene_ID
  </code></pre>
  
  <h3>Question Details &amp; requirements</h3>
  
  <p>Essentially, I have a yeast  <a href="https://yeastmine.yeastgenome.org/yeastmine/begin.do" rel="nofollow noreferrer">database</a> with gene expression information (where the gene names are named in the <em>S. cerevisiae</em> convention <sup>eg</sup> YMR105C or YDL204W) and I'm trying to relate each of those expression profiles to their respective homologous gene in my species of yeast.</p>
  
  <p>I've exported the systemic file names (and their respective protein residue sequences) for <em>S. cerevisiae</em>, turned that into a big fasta file (~6,000 sequences) and then run a tBLASTn against my yeast genome to give a single Report page where you select each submitted FASTA sequence from the "Results for:" dropdown and it brings up the alignments for that specified sequence as normal. To manually curate this would take forever and I was wondering if there's a way to generate a table containing all the results where the E-value is below a certain threshold?
  Ideally it'd be something along the lines of:</p>
  
  <p>"FASTA Name"  "Max score"  "Total score"  "Query cover"  "E value" "Identity" 
   "Accession" "Gene*"</p>
  
  <p>*where "Gene" is what you get when you get the title of the page if you were to click that specific "Accession" hyperlink... appreciate that might be beyond the scope of this question though.</p>
  
  <p>Is this possible (or indeed is there a completely different strategy) or should do I need to download the relevant databases and run something along the lines of <a href="https://www.biostars.org/p/5684/" rel="nofollow noreferrer">this</a>?</p>
  
  <p>Thanks for all your help in advance!</p>
  
Tags: <public-databases><phylogenetics><blastp>
Title: How to export web NCBI tBLASTn results in table format with many queries?
ThreadText: # How to export web NCBI tBLASTn results in table format with many queries?
  
  (Asked by: username_0 on 2018-12-24)
  
  ### Context
  
  I'm an MSc student working on writing up my thesis (back home now) from my laptop and, therefore, unfortunately don't have access to a workstation/server capable of doing the tBLASTn search that I wanted to do. As a result I have been trying to use as many online resources as possible.
  
  ### Question
  
  Is there a way to export the tBLASTn results from the NCBI website to a simple text file? I want the output to be something similar to:
  
  ```
  FASTA_Name Max_score Total_score Query_cover E_value Identity Accession Gene_ID
  
  ```
  
  ### Question Details & requirements
  
  Essentially, I have a yeast [database](https://yeastmine.yeastgenome.org/yeastmine/begin.do) with gene expression information (where the gene names are named in the *S. cerevisiae* convention eg YMR105C or YDL204W) and I'm trying to relate each of those expression profiles to their respective homologous gene in my species of yeast.
  
  I've exported the systemic file names (and their respective protein residue sequences) for *S. cerevisiae*, turned that into a big fasta file (~6,000 sequences) and then run a tBLASTn against my yeast genome to give a single Report page where you select each submitted FASTA sequence from the "Results for:" dropdown and it brings up the alignments for that specified sequence as normal. To manually curate this would take forever and I was wondering if there's a way to generate a table containing all the results where the E-value is below a certain threshold?
  Ideally it'd be something along the lines of:
  
  "FASTA Name" "Max score" "Total score" "Query cover" "E value" "Identity"
  "Accession" "Gene\*"
  
  \*where "Gene" is what you get when you get the title of the page if you were to click that specific "Accession" hyperlink... appreciate that might be beyond the scope of this question though.
  
  Is this possible (or indeed is there a completely different strategy) or should do I need to download the relevant databases and run something along the lines of [this](https://www.biostars.org/p/5684/)?
  
  Thanks for all your help in advance!
  
  **Tags:** public-databases, phylogenetics, blastp
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2018-12-24. Score: 5
  
  It sounds like your easiest option is to just install blast on your local machine and set up the databases there. It really will only take a few minutes to blast 6,000 sentences against a yeast genome on a modern laptop. Any solution interfacing with web results or parsing the output will be painfully convoluted. There are executables for blast that will work on Mac, Linux, or Windows.
  
  Some beginning instructions for installing it on your laptop can be found here: <https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download> . Make sure to pass the --num\_threads option to speed up the search.
  
  
  ---
  
  