Jun 28 2018 Feedback.
Contents
 
Introduction
Help Videos
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
 Read and Save
 Secondary Structure
 Bioinfo Menu
 BLAST Search
 Sequence Editor
 Alignments
 Editor
 Color Structure by Alignment
Protein Modeling
Cheminformatics
Learn and Predict
Docking
Virtual Screening
MolScreen
3D Ligand Editor
Tables and Plots
Local Databases
ICM-Scarab
KNIME
Tutorials
FAQs
 
Index
PrevICM User's Guide
8.4 BLAST Search
Next

Available in the following product(s): ICM-Pro

To BLAST the NCBI sequence database (including PDB sequences):

  • Go to the Search tab
  • Choose the drop down option for BLAST and follow the instructions here.

To BLAST search a local BLAST formatted file:

ICM provides a fast tool to search any Blast-formatted database with a query sequence and generate an alignment on the fly. For example you can use this option to find template structures for homology modeling.

  1. Select Bioinfo/Search and Align (or right click on a sequence)
  2. Enter the sequence name you wish to search against the database with.
  3. Locate the blast-formatted database to search. You can download Blast formatted databases from here ftp://ftp.ncbi.nih.gov/blast/db/ eg. pdbaa - PDB sequence database.
  4. Specify the speed parameter (0 is the slowest, but the most detailed, 100 is the fastest search for nearly identical sequences).
  5. Enter the number of hits you would like to view
  6. Enter an identity threshold filter to narrow down the number of hits.
  7. The top hits will be displayed in a table.


Prev
Load Example Alignment
Home
Up
Next
Sequence Editor

Copyright© 1989-2018, Molsoft,LLC - All Rights Reserved.
This document contains proprietary and confidential information of Molsoft, LLC.
The content of this document may not be disclosed to third parties, copied or duplicated in any form,
in whole or in part, without the prior written permission from Molsoft, LLC.