meta data for this page
  •  

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
general:computerenvironment:blastp [2019/05/07 11:05] – rubengeneral:computerenvironment:blastp [2025/05/08 09:24] (current) – freya
Line 3: Line 3:
 Use this to find sequence similarity of your favorite protein in a database of proteins, for example, in the proteome of another organism. Alternative to the [[https://blast.ncbi.nlm.nih.gov/Blast.cgi|NCBI BLAST]] server, it can also be ran locally with the command line. Use this to find sequence similarity of your favorite protein in a database of proteins, for example, in the proteome of another organism. Alternative to the [[https://blast.ncbi.nlm.nih.gov/Blast.cgi|NCBI BLAST]] server, it can also be ran locally with the command line.
 Example sequence for BLAST.  Example sequence for BLAST. 
-<hidden>+<code>
 >HSP70B >HSP70B
 MPVQQMTSMRSQSLAGAPVAPVKAGRAGVSRRGLAVSVRAEKVVGIDLGTTNSAVAAMEG MPVQQMTSMRSQSLAGAPVAPVKAGRAGVSRRGLAVSVRAEKVVGIDLGTTNSAVAAMEG
Line 17: Line 17:
 AKLGELKAALPADDAEATKAAMNALQQEVMAMGQAMYSQAGAAPGGAPGAEPGAGAGAGG AKLGELKAALPADDAEATKAAMNALQQEVMAMGQAMYSQAGAAPGGAPGAEPGAGAGAGG
 APGGKKDDDVIDAEFTDKK APGGKKDDDVIDAEFTDKK
-</hidden>+</code>
  
 ===== Locally with the command line ===== ===== Locally with the command line =====
Line 34: Line 34:
 blastp -query ../secuencias_query.fasta -db chlamydomonas -out ../resultados_blastp.txt -evalue 0.05 -outfmt "6 std qcovs" blastp -query ../secuencias_query.fasta -db chlamydomonas -out ../resultados_blastp.txt -evalue 0.05 -outfmt "6 std qcovs"
 </code> </code>
- 
-ACHTUNG: As [[https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty833/5106166|Andreas pointed out]], the option "-max_target_seqs 1" will not prompt the best result, but the first result to make a hit. 
  
 BLASTp output by column. Information of BLAST terms can be found in the [[https://www.ncbi.nlm.nih.gov/books/NBK62051/|glossary]]. BLASTp output by column. Information of BLAST terms can be found in the [[https://www.ncbi.nlm.nih.gov/books/NBK62051/|glossary]].
Line 53: Line 51:
   - Coverage   - Coverage
  
 +/*
 ===== Filter your results ===== ===== Filter your results =====
  
Line 70: Line 69:
  
   * The Bitscore is another indicator, but in contrast to the e-value, it is independent of sequence length and database size.   * The Bitscore is another indicator, but in contrast to the e-value, it is independent of sequence length and database size.
 +*/
 ===== Noted issues ===== ===== Noted issues =====