Answers.Body: <p>You should increase the <code>-evalue 10</code> default option to a higher value because this value it's adjusted to the sequence database size. Check this table, maybe this can help you to decide which parameters are the best option for you.</p>
  
  <pre><code>    OPTION      TASK          DEFAUL    DESCRIPTION
      word_size   blastp        3         Word size of initial match.
      word_size   blastp-short  2         Word size of initial match.
      gapopen     blastp        1         Cost to open a gap.
      gapopen     blastp-short  9         Cost to open a gap.
      gapextend   blastp        1         Cost to extend a gap.
      gapextend   blastp-short  1         Cost to extend a gap.
      matrix      blastp        BLOSUM62  Scoring matrix name.
      matrix      blastp-short  PAM30     Scoring matrix name.
      threshold   blastp        11        Minimum score to add a word to the BLAST lookup table.
      threshold   blastp-short  16        Minimum score to add a word to the BLAST lookup table.
      window_size blastp        40        Multiple hits window size, use 0 to specify 1-hit algorithm.
      window_size blastp-short  15        Multiple hits window size, use 0 to specify 1-hit algorithm.
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-21T20:40:47.187Z
Answers.Text: Thanks! Can you please explain what is the meaning of `word_size` and `window_size` in the parameters?
Answers.UserDisplayName: Mahasish
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-21T21:20:37.207Z
Answers.Text: The `word_size` parameter is used in the initial search when BLAST makes a table of all possible "words" present in the query sequence. This first search is not only for identical "words" but for all "words" that would yield an alignment with a score above a threshold, with this step, BLASTp increases speed at the expense of only a small loss in sensitivity by only trying to extend a "hit" if there is a second "hit" within a certain `window_size`.
Answers.UserDisplayName: zorbax
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-22T23:43:35.573Z
Answers.Text: How does `word_size` effects my BLASTp result? If I want to find 5 or 6 amino acid match at least then increasing `word_size` to 5 or 6 will help? It means it will try to find 5 or 6 amino acids initial match?
Answers.UserDisplayName: Mahasish
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-21T02:27:26.683Z
Answers.LastActivityDate: 2020-03-21T02:27:26.683Z
Answers.UserDisplayName: zorbax
Body: <p>I am trying to find sequence homology between viral sequences and my protein of interest. I have the sequences of their epitopes which varies from 5 to 500 amino acids long. For shorter sequences, it is recommended to use <code>blastp-short</code> but I am confused until which length it is okay to run <code>blastp</code>?</p>
  
  <p>For shorter sequences, what are the parameters needs to be added for effective results?</p>
  
  <p><code>blastp -task blastp-short -query POI.fasta -db virus.fasta -out output.txt -outfmt 6 -evalue 20000</code></p>
  
Tags: <phylogenetics><blast><covid-19><sequence-homology><blastp>
Title: How to do BLASTP for short sequences (<20 aa) effectively?
ThreadText: # How to do BLASTP for short sequences (<20 aa) effectively?
  
  (Asked by: username_0 on 2020-03-21)
  
  I am trying to find sequence homology between viral sequences and my protein of interest. I have the sequences of their epitopes which varies from 5 to 500 amino acids long. For shorter sequences, it is recommended to use `blastp-short` but I am confused until which length it is okay to run `blastp`?
  
  For shorter sequences, what are the parameters needs to be added for effective results?
  
  `blastp -task blastp-short -query POI.fasta -db virus.fasta -out output.txt -outfmt 6 -evalue 20000`
  
  **Tags:** phylogenetics, blast, covid-19, sequence-homology, blastp
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-03-21. Score: 1 | Accepted answer
  
  You should increase the `-evalue 10` default option to a higher value because this value it's adjusted to the sequence database size. Check this table, maybe this can help you to decide which parameters are the best option for you.
  
  ```
      OPTION      TASK          DEFAUL    DESCRIPTION
      word_size   blastp        3         Word size of initial match.
      word_size   blastp-short  2         Word size of initial match.
      gapopen     blastp        1         Cost to open a gap.
      gapopen     blastp-short  9         Cost to open a gap.
      gapextend   blastp        1         Cost to extend a gap.
      gapextend   blastp-short  1         Cost to extend a gap.
      matrix      blastp        BLOSUM62  Scoring matrix name.
      matrix      blastp-short  PAM30     Scoring matrix name.
      threshold   blastp        11        Minimum score to add a word to the BLAST lookup table.
      threshold   blastp-short  16        Minimum score to add a word to the BLAST lookup table.
      window_size blastp        40        Multiple hits window size, use 0 to specify 1-hit algorithm.
      window_size blastp-short  15        Multiple hits window size, use 0 to specify 1-hit algorithm.
  
  ```
  
  > **Comments:**
  > **username_0**: Thanks! Can you please explain what is the meaning of `word_size` and `window_size` in the parameters?  
  > **username_1**: The `word_size` parameter is used in the initial search when BLAST makes a table of all possible "words" present in the query sequence. This first search is not only for identical "words" but for all "words" that would yield an alignment with a score above a threshold, with this step, BLASTp increases speed at the expense of only a small loss in sensitivity by only trying to extend a "hit" if there is a second "hit" within a certain `window_size`.  
  > **username_0**: How does `word_size` effects my BLASTp result? If I want to find 5 or 6 amino acid match at least then increasing `word_size` to 5 or 6 will help? It means it will try to find 5 or 6 amino acids initial match?  
  
  ---
  
  