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:
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
- 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.