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Igor B. Kuznetsov
Software developed in our lab
BIAS: software and web-server for the identification of user-defined types of
compositional bias in biological sequences
Source code and binaries: http://lcg.rit.albany.edu/bias/
Web-version: http://lcg.rit.albany.edu/ProBias/ |
DP-Bind: a web-server for sequence-based prediction of
DNA-binding residues
in DNA-binding proteins
The server uses a protein sequence to run three prediction methods and calculates a consensus prediction: http://lcg.rit.albany.edu/dp-bind/ |
CFP: a web-server for the identification of protein segments with
high backbone flexibility
The server uses a protein sequence to identify potential conformationally flexible segments:
http://cfp.rit.albany.edu |
FlexPred: a web-server for predicting residue positions involved in
conformational switches in proteins
The server accepts either a protein sequence or a PDB file to predict residue positions involved in conformational switches:
http://flexpred.rit.albany.edu |
NAT2PRED: a web-server for predicting the human
N-AcetylTransferase-2 acetylator phenotype
The server predicts the activity level of the human N-AcetylTransferase-2 (NAT2) based on
the combination
of single nucleotide polymorphisms (SNPs) observed in the NAT2 gene:
http://nat2pred.rit.albany.edu
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SP2ALIGN: software and a web-server for pair-wise alignment of amino acid sequences by using weighted profiles of biochemical properties
This web-server finds an optimal global alignment of two amino acid sequences by utilizing weighted profiles of their biochemical properties instead of a single similarity matrix:
http://sp2align.rit.albany.edu/ |
Software resources
Commercial: MatLab, C/C++ development tools, Perl development tools, Web-development and publishing tools, Statistica, SAS, SPSS, S-Plus, TransFac.
Public domain: R, BioConductor, BioPerl, libSVM, numerical analysis packages, PHP, Python, Apache, SQL, etc.
Hardware resources
Our lab has a number of PCs runing under Windows/Linux operating systems and the following dedicated servers running under Linux operating system:
- One 4x4-processor 64Gb RAM DELL PowerEdge server
- One 4x2-processor 16Gb RAM DELL PowerEdge server
- Two dual-processor DELL PowerEdge servers (6Gb and 4Gb RAM).
- DELL high-performance computing cluster that has 16 compute nodes and a head node. Each node has two IntelXeon processors and 4 Gb RAM.
- All servers are connected to a shared network file system and backed up daily.
- We also have an unlimited access to hundreds of CPUs on shared high-performance Linux clusters maintained by the UAlbany Research IT Department and the New York State Grid.
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