Code covered by the BSD License  

Be the first to rate this file! 16 Downloads (last 30 days) File Size: 32.8 KB File ID: #46071

Sequence Assembly App

by

 

28 Mar 2014 (Updated )

Assemble overlapping sequences according to reference

| Watch this File

File Information
Description

Assembling overlapping sequences, especially with batches of samples, is a difficult task. This app is designed to assist the user in importing sets of sequences by sample into MATLAB, clip them to a common reference sequence (via Smith-Waterman local alignment), determine their overlap (also Smith-Waterman), and assemble them into a single full sequence construct. Sequences can be imported using a pre-formatted FASTA or via sequential copying to the clipboard. After processing, constructs with acceptable length and reference local alignment score can be selected for export. Export options include feeding clipped sequences, nucleotide assemblies, and/or protein translations to FASTA, the Sequence Viewer App, and/or the Sequence Alignment App after multiple global alignment.
Please provide feedback if you find this app useful or if you would like to see any changes/additions.

Required Products Bioinformatics Toolbox
Statistics Toolbox
MATLAB
MATLAB release MATLAB 8.3 (R2014a)
Tags for This File   Please login to tag files.
Please login to add a comment or rating.
Updates
02 Apr 2014

Name changed from forRevAlign to strandAlign; see CHANGELOG section in code for detailed changes.

07 Apr 2014

Implemented as app

12 May 2014

Capabilities greatly improved to allow any number of sequences per sample, automatic strand/reference position detection, and more fluid import/export. Name changed to Sequence Assembly App. See CHANGELOG section in code for details.

22 Jul 2014

Edited description

Contact us