View source for How to generate an HSSP file from alignment

== Disclaimer ==
Please note that the following instructions are an example only and were not widely tested on other systems. It is assumed that all required  ([[profphd | profphd]]) and recommended ([http://blast.ncbi.nlm.nih.gov/blast.cgi?cmd=web&page_type=blasthome blast2]) packages were installed in system space of the target machine. Deviation from these assumptions may result in abnormal operation. Please use discretion when applying this example.

== Generating an HSSP profile ==
Generating an HSSP profile requires converting a blast alignment to an HSSP profile. The following example shows how this is done for the [http://www.predictprotein.org PredictProtein server].

Debian/Ubuntu package providing below programs: 'librg-utils-perl'.

1. Convert BLAST output to a Single Alignment Format (SAF):

Either (recommended)
 /usr/share/librg-utils-perl/blast2saf.pl fasta=<query_fasta_file> eSaf=1 \
  saf=<saf_formatted_file> <blast_output>
- or -
<div style="font-size:smaller"><div style="font-size:smaller">
<span style="color:orange;background-color:red;font-weight:bold;">This method is being phased out. The above code is in better shape and has more features, like E-value filtering.</span>
 /usr/share/librg-utils-perl/blastpgp_to_saf.pl fileInBlast=<blast_output> fileInQuery=<sequence_file> \
  fileOutRdb=<alignment_formatted_as_table_output_file> fileOutSaf=<saf_formatted_file> \
  red=100 maxAli=3000 tile=0
</div></div>

2. Convert SAF format to HSSP:
 /usr/share/librg-utils-perl/copf.pl <saf_formatted_file> formatIn=saf formatOut=hssp \
  fileOut=<hssp_formatted_file> exeConvertSeq=convert_seq 

3. Filter results to 80% redundancy:
 /usr/share/librg-utils-perl/hssp_filter.pl red=80 <hssp_formatted_file> fileOut=<'''filtered'''_hssp_formatted_file>

* blast2saf.pl can be used to reduce the number of sequences in the alignment like this: <code>red=80 maxAli=3000</code> (<code>maxAli</code> is only effective when <code>red != 100</code>).