ICM-Bioinformatics

The ICM-Bioinformatics module provides the environment for manipulations with sequences, alignments, profiles and databases both interactively and in a batch mode. It also provides direct connectivity with 3D models.

Accurate pairwise alignments and their significance: ICM includes two high-quality global pairwise alignment algorithms with zero-end penalties (ZEGA). double-affinity gap penalties and dual insertions. Also an empirical statistics was derived for many residue substitution matrices and gap penalties to evaluate the probabbility that the two aligned sequences share the same structural fold. This statistics can also be used locally to evaluate the local reliability of an alignment, or identify the alternative alignments and repeats in probability weighted dot-plot.

ZEGA-based database searches for distance relatives and structural similarities. The sensitive and rigorous Zega alignment is used for each comparison, and the structural statistics identifies the significant hits. This search may give you more homologues than a BLAST search! The output may be presented in a linked table form:

Table of hits:

NA1 NA2 ID SC pP DE
Fyn 1nyf_mNo 100. 62.81 20.94 Fyn
Eps8 1tud_m17 21. 17.04 4.17 alpha-spectrin
Eps8 1fyn_a23 22.6 17.02 4.16 Phosphotransferase fyn
Eps8 1efn_a25 22. 16.64 4.11 Fyn tyrosine kinase
Eps8 1hsq_mNo 24.2 16.87 4.1 Phospholipase c-gamma (sh3 domain)

Pattern searches, prosite and profile searches, other functions. Other functions include tools for indexing and quering the flat-file sequence databases, annotation transfer functions, sequence-structure connectivity.

Multiple Sequence Alignments and principal component clustering: Accurate pairwise sequence-sequence, sequence-profile and profile –profile alignments are used to build multiple sequence alignments with a hierachical, evolutionary tree-guided, alignment procedure. Better pairwise alignments, neighbor-joining tree construction algorithm and weighted profile construction leads to high-quality alignments. The shell allows to generate them in batch and control all the alignment parameters.

Sequence Structure Alignment: Use an interactive alignment editor for easy alignment and tether editing. Color your selections for easy identification. Relationships between sequences can be shown as evolutionary trees from the specified sequence alignment using the neighbor-joining method (Saitou and Nei, 1987), as 2D distribution of sequences using the two main principal axes, and as 3D distribution. This can be analyzed in stereo using controls of molecular graphics. Create a PostScript images of your results.

Sequence-Structure Alignment for Homology Modeling: Both the secondary structure and the template 3D structure are used for sequence threading. Search your sequence interactively or in batch through any database and generate a list of possible homologues which are sorted and evaluated by probability of structural significance. Use this alignment in homology modeling.

Platforms Available : Windows XP/NT/2000, Linux/i386/AMD64, SGI IRIX, Mac OS X