Contract Research Tools
Fragment Analysis
Peak Scanner Software v1.0 (PC: Free)
This easy-to-use software analyses separated DNA fragments by size, provides a profile of the separation,
and precisely calculates each fragment size. The user can view, edit, analyze, print, and export fragment
analysis data generated on all Applied Biosystems Genetic Analyser platforms.
STRand, Nucleic Acid Analysis Software
STR Analysis Software for fragment analysis.
Sequencing
Chromas
(PC: £)
Opens chromatogram files from Applied Biosystems and Amersham
MegaBace DNA sequencers and view Genescan genotype files.
Save in SCF or Applied Biosystems format and exports sequences
in plaint text, formatted with base numbering, FASTA, EMBL,
GenBank or GCG formats. Reverse & complement the sequence
and chromatogram, search for sequences by exact matching or
optimal alignment. Display translations in 3 frames along
with the sequence.
Edit
View (Mac OS9: free)
Macintosh users can download a copy of
the FREE Applied Biosystems program Edit View from the this web site.
Please click on the link below to initiate download of Stuffit (.sit) archive.
You will need a copy of the Stuffit Expander application to decode this file.
FinchTV (PC, Mac, Linux: Free)
Geospizas FinchTV is the popular way to view DNA sequence traces on Linux,
Mac OSX, Windows, and Solaris. FinchTV started as the only chromatogram viewer that can display an
entire trace in a scalable multipane view. Now it leads again with raw data views, BLAST searching
and the ability to reverse complement sequences and traces.
Jemboss (PC, Mac, Linux: Free)
EMBOSS, The European Molecular Biology Open Source Software Suite, is a package of
high-quality FREE Open Source software for sequence analysis. Jemboss is a java viewer for emboss.
Staden (PC, Unix: Free)
The Assembly program Gap4 performs assembly,
contig joining, assembly checking, repeat searching, experiment suggestion, read pair analysis
and contig editing. Has graphical views of contigs, templates, readings and traces which all
scroll in register. Contig editor searches and experiment suggestion routines use phred confidence
values to calculate the confidence of the consensus sequence and hence only identify places
requiring visual trace inspection or extra data. The result is extremely rapid finishing and
a consensus of known accuracy. Pregap4 prepare sequence trace data for analysis or assembly
and provides a graphical user interface to set up the processing required to prepare trace
data for assembly or analysis; and also gives a method for its automation. The possible
processes which can be set up include trace format conversion, quality analysis, vector
clipping, contaminant screening and repeat searching.
PC to Mac conversion utiliy (Mac: Free)
ABI has now moved to Windows PC as their computer standard. Mac users need to convert their sequencer files as follows:
- Download and save "ConvProg.sit" from Applied Biosystems
- Expand the file to a folder "ConvProg Folder" using StuffIt Expander
- Convert the PC electropherogram files from Windows format to Mac format using the conversion program "Sample File Win to Mac" in the ConvProg Folder:
- Double click to launch the conversion program "Sample File Win to Mac".
- Select the folder (NOT THE INDIVIDUAL FILES INSIDE THE FOLDER) generated from the above step 3), which contains the expanded sequencing results to be converted.
- Click "Choose". The files will be converted in the folder automatically.
Real Time PCR
SDS software for Real Time PCR (PC: Free)
SDS 1.2.3 - Real Time PCR Analysis Software
Tm Calculator (PC: Free)
Tm Calculator - Useful tool for calculating primer Tm's
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