<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>

CC BY-SA 4.0
2020-03-21T20:40:47.187Z
Thanks! Can you please explain what is the meaning of `word_size` and `window_size` in the parameters?
Mahasish
CC BY-SA 4.0
2020-03-21T21:20:37.207Z
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`.
zorbax
CC BY-SA 4.0
2020-03-22T23:43:35.573Z
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?
Mahasish
CC BY-SA 4.0
2020-03-21T02:27:26.683Z
2020-03-21T02:27:26.683Z
zorbax
<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>

<phylogenetics><blast><covid-19><sequence-homology><blastp>
How to do BLASTP for short sequences (<20 aa) effectively?
# 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

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## 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?  

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