File Exchange

Sequence Assembly App

version 1.4 (32.8 KB) by

Assemble overlapping sequences according to reference



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.

Comments and Ratings (0)



Edited description


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.


Implemented as app


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

MATLAB Release
MATLAB 8.3 (R2014a)

Download apps, toolboxes, and other File Exchange content using Add-On Explorer in MATLAB.

» Watch video

Win prizes and improve your MATLAB skills

Play today