Sequence Assembly App

Assemble overlapping sequences according to reference
727 Downloads
Updated 22 Jul 2014

View License

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.

Cite As

Turner Conrad (2024). Sequence Assembly App (https://www.mathworks.com/matlabcentral/fileexchange/46071-sequence-assembly-app), MATLAB Central File Exchange. Retrieved .

MATLAB Release Compatibility
Created with R2014a
Compatible with any release
Platform Compatibility
Windows macOS Linux
Categories
Find more on Genomics and Next Generation Sequencing in Help Center and MATLAB Answers

Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!
Version Published Release Notes
1.4.0.0

Edited description

1.3.0.0

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.

1.2.0.0

Implemented as app

1.1.0.0

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

1.0.0.0