Bioinformatics Tools

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ICM-Bioinformatics is included in the ICM-Pro package allows users to search a sequence database with high-quality global pairwise and multiple alignment algorithms. Also allows pattern searches, prosite and profile searches. Multiple sequence alignments are fast, the algorithm produces evolutionary trees, principal component view, annotation transfer from sequence to structures, threading and alignment visualization tools. Sequence Analysis: Find alternative alignments and repeats using filtered and probability based dot-plot. Make accurate pairwise sequence alignment with a double affine gap penalty and evaluate the probability that the two aligned sequences share the same structural fold. Build multiple sequence alignments, construct and plot evolutionary trees, visualize sequence clustering in two and three dimensions, predict protein secondary structure with a set of powerful algorithms. Search your sequence interactively or in batch through any database and generate a list of possible homologues that are sorted and evaluated by probability of structural significance. The sensitive and rigorous Zega alignment is used for each comparison. This search may give you more homologues that a BLAST search! The output may presented in a linked table form. The text sequence databases can be indexed and queried with ICM. Return to Main ICM-Pro Page

Key Bioinformatics Features

Sequence Analysis

Read in sequences and alignment in many different formats including FASTA.

Direct link to the UniProt sequence database.

Direct link to PFam.

Calculate sequence residue content a table and graph of residue frwequencies will be displayed.

Predict sequence secondary structure.

Six frame translation.

Set sequence type e.g Protein or DNA.

Fully interactive sequence editor.

Save sequence as an image.

Save a sequence in a variety of formats.

Sequence Alignments

Align two sequences.

Seven alignment comparison matrices to choose from.

A variety of alignment methods available including ZEGA, H-align, Needleman-Wunsch, Smith-Waterman and Wilbur-Lipman.

Adjust parameters such as Gap Open, Gap Extension.

Perform sequence to structure alignment.

Align DNA to Protein.

Multiple Sequence Alignments

Dynamic and feature-rich multiple sequence alignment editor.

Easy drag and drop alignment construction.

Link the alignment to 3D protein structures in the graphical display. e.g. select a region in the alignment and this selection will be propogated onto the protein structure.

Extract a sub alignment.

Cut a vertical alignment block.

Reorder sequences in an alignment.

Extract unique sequences.

Hide/Show gaps in the alignment.

Compress gaps in the alignment.

Search in an alignment.

Save and export a high quality image of the alignment.

Copy the alignment to clipboard.

Build a residue number table of the alignment.

Build a residue label table of the alignnent.

Cut a selected block of an alignment.

Make a sequence QSAR table.

Copy and paste selected regions of an alignment.

Annotate regions of an alignment.

Shade regions of an alignment.

Change the font color in an alignment.

Set fonts to bold.

Draw a box around a region of an alignment.

Add a title to an alignment.

Display the consensus sequence of the alignment.

Display the sequence profile at each point of the alignment.

Display sequence ruler.

Display sequence tree.

Display the sequences in the alignment as unaligned.

View differences in the alignment.

Color the alignment by a variety of built-in and user-defined color schemes. For example you can adjust the consensus strength and color or color by hydrophobicity.

Make complex selections in the alignment. This is helpful when the alignment is linked to a 3D structure.

Display sequence secondary structure.

Sequence Search

ICM-Pro provides a fast tool to search any Blast-formatted database with a query sequence and generate an alignment on the fly.

Search by sequence similarity.

Search by sequence homology.

Return to Main ICM-Pro Page