SeqTrace 0.9.0 – Rapidly Processing DNA Sequencing Chromatograms

SeqTrace 0.9.0

:: DESCRIPTION

SeqTrace is an application for viewing and processing DNA sequencing chromatograms (trace files). SeqTrace makes it easy to quickly generate high-quality finished sequences from a large number of trace files. SeqTrace can automatically identify, align, and compute consensus sequences from matching forward and reverse traces, filter low-quality base calls, and perform end trimming of finished sequences. The finished DNA sequences can then be exported to common sequence file formats, such as FASTA.

::DEVELOPER

Brian J. Stucky  stuckyb@colorado.edu , Guralnick Lab

:: SCREENSHOTS

SeqTrace 

:: REQUIREMENTS

  • Linux/ MacOsX/ Windows 
  • Python
  • PyGTK with the GTK+

:: DOWNLOAD

 SeqTrace

:: MORE INFORMATION

Citation

J Biomol Tech. 2012 Sep;23(3):90-3. doi: 10.7171/jbt.12-2303-004.
SeqTrace: a graphical tool for rapidly processing DNA sequencing chromatograms.
Stucky BJ.

Chromaligner – Chromatogram Alignment

Chromaligner

:: DESCRIPTION

Chromaligner is a tool for chromatogram alignment. It could be used for chromatograms generated by various chromatographic methods such as high performance liquid chromatography and capillary electrophoresis. Time shift is a frequent encountered problem in gradient elution or capillary electrophoresis. Chromaligner used a constrained chromatogram alignment method to resolve this issue.

::DEVELOPER

Chromaligner team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Sep 15;26(18):2338-9. doi: 10.1093/bioinformatics/btq337. Epub 2010 Jun 23.
Chromaligner: a web server for chromatogram alignment.
Wang SY1, Ho TJ, Kuo CH, Tseng YJ.

DIAlignR v1.1.2 – Chromatogram Alignment for Targeted Proteomics

DIAlignR v1.1.2

:: DESCRIPTION

DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.

::DEVELOPER

Röst Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX
  • R

:: DOWNLOAD

DIAlignR

:: MORE INFORMATION

Citation

Gupta S, Ahadi S, Zhou W, Röst H.
DIAlignR Provides Precise Retention Time Alignment Across Distant Runs in DIA and Targeted Proteomics.
Mol Cell Proteomics. 2019 Apr;18(4):806-817. doi: 10.1074/mcp.TIR118.001132. Epub 2019 Jan 31. PMID: 30705124; PMCID: PMC6442363.

ChromatoGate 1.2 – Analyze / Edit Chromatogram data

ChromatoGate 1.2

:: DESCRIPTION

ChromatoGate (CG) has been created to accelerate the process of detecting possible errors in DNA sequences that have been introduced by Sanger sequencers. To detect possible errors in the sequences, CG starts from the multiple-sequence alignment instead of inspecting every sequence separately.

::DEVELOPER

the Exelixis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 ChromatoGate

:: MORE INFORMATION

Citation

ChromatoGate: A Tool for Detecting Base Mis-Calls in Multiple Sequence Alignments by Semi-Automatic Chromatogram Inspection
Nikolaos Alachiotis, Emmanouella Vogiatzi, Pavlos Pavlidis, Alexandros Stamatakis
7th conference of the Hellenic Society for Computational Biology and Bioinformatics Volume No: 6, Issue: 7, March 2013, e201303001,

Chromas 2.6.6 / ChromasPro 2.1.8 – Sequence & Chromatogram Editor

Chromas 2.6.6 / ChromasPro 2.1.8

:: DESCRIPTION

Chromas is a low-cost chromatogram file editor with search, vector sequence detection and multi-format sequence export functions, plus powerful batch processing.

ChromasPro is a low-cost sequence and chromatogram editor with search, vector sequence detection, contiguous sequence assembly and restriction and open-reading-frame mapping.

::DEVELOPER

Technelysium Pty Ltd

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Chromas ,  ChromasPro

:: MORE INFORMATION

MassChroQ 2.0.1 – Mass Chromatogram Quantification

MassChroQ 2.0.1

:: DESCRIPTION

MassChroQ is a fast and versatile software that performs alignment, XIC extraction, peak detection and quantification on data obtained from Liquid Chromatography-Mass Spectrometry (LC-MS) techniques.

::DEVELOPER

pappso (Plate-forme d’analyses protéomiques de Paris Sud-Ouest)

:: SCREENSHOTS

MassChroQ

:: REQUIREMENTS

  • Windows/ MacOsX / Linux
  • Java

:: DOWNLOAD

 MassChroQ

:: MORE INFORMATION

Citation

Valot B, Langella O, Nano E, Zivy M, (2011),
MassChroQ: A versatile tool for mass spectrometry quantification,
Proteomics, 11:3572-3577.

DNA Chromatogram Explorer Lite 3.2 – View, Edit & Convert Chromatogram

DNA Chromatogram Explorer Lite 3.2

:: DESCRIPTION

DNA Chromatogram Explorer is a Windows Explorer clone dedicated to DNA sequence analysis and manipulation. You can view the chromatograms while browsing through folders using its integrated file explorer. With a single click you can trim the low quality bases at the end of your samples. The Lite version of Chromatogram Explorer is freeware.

::DEVELOPER

Heracle BioSoft

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

DNA Chromatogram Explorer Lite

:: MORE INFORMATION

N/A