The PSI-BLAST Intermediate Sequence Search tool: PSI-BLAST-ISS

The Intermediate Sequence Search (ISS) tool is designed to assess the region-specific alignment reliability between two or more protein sequences (target and template(s)). The main idea of the algorithm is to initiate additional PSI-BLAST searches against the non-redundant sequence database for a set of sequences that are related both to the target and to the template(s). The position- specific reliability of the alignment between the target and the template(s) is then assessed by merging alignment data obtained from intermediate sequence searches and analyzing alignment convergence.

Download the recent version of the psi-blast-iss tool,

iss-v1.04.tar.gz [version 1.04]


The older versions:

iss-v1.03.tar.gz [version 1.03]

iss-v1.02.tar.gz [version 1.02]

iss-v1.01.tar.gz [version 1.01]

iss-v1.0.tar.gz [version 1.0]


To install the tool, download the package to your local directory, uncompress and untar it by running the command

tar -zxvf iss-v<ver_num>.tar.gz


Then follow the instructions in the README.install file.



Margelevicius M., Venclovas C. (2005) PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability. BMC Bioinformatics 6(1):185