Operations performed by Command buttons

DNA Commands

• Translate - Translates a given sequence in all six reading frames. Default display is from the 5'-3' in forward direction. Stop codons are indicated by red dots
• ORF - Returns a graphical display of all possible Open Reading Frames using NCBI ORF finder
• View NCBI page - Seen only in 'Results' palette - Displays the NCBI record of a selected sequence from a BLAST report

• DNA pattern - Identifies user defined-annotated sequences within an input sequence. Tool adapted from Sequence Manipulation Suite.

• DNA stats - Provides statistics of the bases in an input sequence. Tool adapted from Sequence Manipulation Suite
• CpG islands - Searches for CpG islands in an input sequence. Tool adapted from Sequence Manipulation Suite.
• Gel Mobility - provides a gel digest pattern of an input sequence cut with any restriction enzyme. Tool adapted from REBASE.
• Map - Provides a linear restriction map of an input sequence with all known restriction enzymes. Tool adapted from REBASE.
• Re-Blast - Runs a BLAST on an input sequence against REBASE. Tool adapted from REBASE.

Protein Commands

• View Structure - Seen only in 'Results' palette - Allows viewing a 3D structure of a selected record from BLAST report that displays a PDBid
• ProtParam - Returns all physicochemical parameters of an input peptide sequence from ExPASy server.
• View NCBI page - Seen only in 'Results' palette - Displays the NCBI record of a selected sequence from a BLAST report
• Prot Stats - Returns statistical results on amino acid composition of an input sequence. Tool adapted from Sequence Manipulation Suite.
• Protein pattern - Identifies user defined-annotated sequences within an input sequence. Tool adapted from Sequence Manipulation Suite.
• Dipole Moment -  Seen only in 'Results' palette - Provides electrostatic surface features of a Functional Site from BLAST report that displays a PDBid. Tool linked to Dipole Moment Server.
• ef Site - Seen only in 'Results' palette - Calculates dipole moment of protein structures from BLAST report that displays a PDBid. Tool linked to eF-Site
• 2˚ Structure Prediction - Predicts secondary structure of a protein of an input sequence. Tool linked to SMART
• NLS predict - Predicts sites containing Nuclear Localization Signals in an input sequence. Tool linked to NLS predict

© copyright 2004. All rights reserved. Created and maintained by Natarajan Ganesan.