Blast Results: Xml Tags Explained ?

Question

[Pasta]

Hi there,

I would like to know if there is any description of the tags that are found in the XML file generated by blastall. I just cannot find any comprehensive document on the web .

More precisely, I would like the difference between: Hsp_score, Hsp_identity and Hsp_positive. I always seem to have the same values...

Thanks for your help

Answer 1

[Niek De Klein]

Hsp_identity is the amount of identical residues between query and subject sequence (over the Hsp part). Hsp_positiv is the amount of residues that are alike (so identicals + if both are hydrophobic or both are hydrofillic for example)

The score is the alignment score, info about that you can find here: (http://searchlauncher.bcm.tmc.edu/help/AlignmentScore.html)

Also very handy: http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new_view.html

Answer 2

[Pierre Lindenbaum]

The description is provided in the XML schema for BLAST: http://www.ncbi.nlm.nih.gov/data_specs/schema/NCBI_BlastOutput.mod.xsd

<xs:element name="Hsp">
  <xs:complexType>
    <xs:sequence>
<!-- HSP number -->
      <xs:element name="Hsp_num" type="xs:integer"/>
<!-- score (in bits) of HSP -->
      <xs:element name="Hsp_bit-score" type="xs:double"/>
<!-- score of HSP -->
      <xs:element name="Hsp_score" type="xs:double"/>
<!-- e-value of HSP -->
      <xs:element name="Hsp_evalue" type="xs:double"/>
<!-- start of HSP in query -->
      <xs:element name="Hsp_query-from" type="xs:integer"/>
<!-- end of HSP -->
      <xs:element name="Hsp_query-to" type="xs:integer"/>
<!-- start of HSP in subject -->
      <xs:element name="Hsp_hit-from" type="xs:integer"/>
<!-- end of HSP in subject -->
      <xs:element name="Hsp_hit-to" type="xs:integer"/>
<!-- start of PHI-BLAST pattern -->
      <xs:element name="Hsp_pattern-from" type="xs:integer" minOccurs="0"/>
<!-- end of PHI-BLAST pattern -->
      <xs:element name="Hsp_pattern-to" type="xs:integer" minOccurs="0"/>
<!-- translation frame of query -->
      <xs:element name="Hsp_query-frame" type="xs:integer" minOccurs="0"/>
<!-- translation frame of subject -->
      <xs:element name="Hsp_hit-frame" type="xs:integer" minOccurs="0"/>
<!-- number of identities in HSP -->
      <xs:element name="Hsp_identity" type="xs:integer" minOccurs="0"/>
<!-- number of positives in HSP -->
      <xs:element name="Hsp_positive" type="xs:integer" minOccurs="0"/>
<!-- number of gaps in HSP -->
      <xs:element name="Hsp_gaps" type="xs:integer" minOccurs="0"/>
<!-- length of the alignment used -->
      <xs:element name="Hsp_align-len" type="xs:integer" minOccurs="0"/>
<!-- score density -->
      <xs:element name="Hsp_density" type="xs:integer" minOccurs="0"/>
<!-- alignment string for the query (with gaps) -->
      <xs:element name="Hsp_qseq" type="xs:string"/>
<!-- alignment string for subject (with gaps) -->
      <xs:element name="Hsp_hseq" type="xs:string"/>
<!-- formating middle line -->
      <xs:element name="Hsp_midline" type="xs:string" minOccurs="0"/>
    </xs:sequence>
  </xs:complexType>
</xs:element>

and the terminology is described here: see http://www.ncbi.nlm.nih.gov/books/NBK62051/#blast_glossary.identity

[Pasta]

Thxxxxxxxxxxxxxxxx !