Accessing Your Sequence Data:
Sequence data is available at the UWBC Facility Files download page. You will log in using your UW-Madison NetID (for campus users) or your email address and UWBC password (for off-campus users). If you haven't used this service before your download directory won't be created until there is sequence data available for your order.
Every effort is made to provide our users with the best data in a timely fashion for the advancement of their research. Turnaround time is typically one working day. If you haven't seen your data on the server by three working days, contact us. Samples that have failed due to gel or capillary problems will of course be rerun free of charge. Usually such problems have a characteristic appearance, so contact us to see if this is where your difficulty might be. Samples are kept seven days, so you must let us know within that time frame if your samples need to be rerun. Our facility handles 4-5,000 samples/week, and despite our best efforts we occasionally make mistakes. If you get data that is completely puzzling (e.g., sequence from an organism that's not even in the same phylum as your model system) please contact us as soon as possible and we can re-run the samples. As above, we need to know within seven days so we can rerun the same samples you brought over. Sometimes we can even trace the problem and give you the correct sequences right away. If the questionable samples are gone, the initial analysis and reanalysis will be done free of charge, and a reasonable attempt made to compensate for reagents wasted.
Stuffit Expander, or another zip utility will be needed to decompress zip files.
Macintosh Conversion Script, will be needed by Mac OS 9 users.
Geneious, provides Windows-Mac-Linux users a single package to store (in an organized fashion), BLAST, document, align, tranlate to amino acid sequence, and create phylogenetic trees, for all their sequence data. It does not yet allow direct import of .ab1 files from the ABI sequencers but apparently this will be possible in future releases. It also performs keyword-based searches for publications related to your sequences and stores them with your sequences.
Sequence Scanner Software v1.0, is a free sequence viewer from Applied Biosystems that allows the user to see the raw data that we see in the facility. It only works on Windows.
Finch Trace View, a newer viewer that is very nice, free, and works on Windows, Mac OS X, and Redhat/SuSE Linux
Xplorer, from dnaTools, also works on Windows and Mac OS X.
Edit View 1.0.1 and 4Peaks, allow Mac users to view their chromatograms.
Chromas, allows Windows users to view their chromatograms.
BioEdit, is a free "sequence alignment editor" for Windows users.
Staden, is a free, open source, genomics package for Windows, Mac OS X 10.3 (see BioX below), and Linux users. It provides tools to do multiple alignments and editing of 1,000s of sequences at a time using simultaneous views of the sequences as text and chromatogram traces, translate consensus sequences in all six reading frames, perform BAC contig alignments, etc.
Invitrogen/Life Technologies is now offering their Vector NTI software to academics. It can be used for sequence alignment, primer design, etc. Be aware, the license is a renewable license.
BioX and ebiotools, is a very powerful, open source, genomics package for Mac OS X 10.3 or above which includes the Staden package, Emboss, clustalw, Blast, T_coffee, and others. The instructions for installing the software are now available on its new site.
We are now using GeneMarker from SoftGenetics to perform all our fragment analyses. It is NOT a free program but ABI no longer supports GeneScan and our copy no longer functions. This has made it impossible for us to perform size calling of size standards for GenoTyper and Genescan. Genemarker is compatible with files from all major capillary and slab gel electrophoresis systems including ABI files (*.FSA, .*AB1, *.ABI), SCF files, MegaBace files (*.RSD, *.ESD), SpectruMedix files (*.SMD, *.SMR), Beckman files, and Licor files. It only runs on Windows.
Peak Scanner, is a free program developed by ABI to aid in fragment analysis. It only runs on Windows.
STRand, is a free program developed to aid in fragment analysis.
To open the electropherogram file, you must acquire trace viewing software. One option is to use an ABI program called EditView (available from our main page). Another good (and free) program is called TraceViewer, and the newest Free program is FinchTV, which can run on most platforms. We recommend playing with the different viewers and seeing which you like best—each has its advantages and disadvantages. Those of you running OS X on your Macs will not be able to use the EditView program, except in the "Classic" mode; Applied Biosystems is not going to update the program to run on OS X. We have seen info on the web indicating there is an updated version of Traceviewer that will work in OS X.
For PC users:
To decompress the Zip file you will need to use a program like Stuffit Expander or WinZip(available from http://dna.biotech.wisc.edu ). After installing you decompression program, simply double click on the Zip file to decompress it.
To view the electropherograms, click on the FinchTV, Chromas or BioEdit links in the Sequence Viewers section of our web site. These programs, once unzipped, will allow you to view the electropherograms. Other places to acquire PC versions of electropherogram viewing programs are http://www.mbio.ncsu.edu/BioEdit/bioedit.html, or www.technelysium.com.au/chromas.html (these are more updated versions of chromas that cost a nominal fee). Finally, a program called Traceviewer from Codon Codes is a decent PC based viewing application (www.codoncode.com).
Some Notes about these programs:
1) Bioedit: Bioedit is a large (~11mb) but FREE program which allows you to view, edit, print your chromatograms as well as many other features such as doing alignments, built in blast searching, etc... This is a highly recommended free program!
2) Chromas is now available in two versions:
a. Version 1.45 is the older FREEWARE version of the software which allows basic viewing, editing, and printing.
b. Version 2.21 is a SHAREWARE version which expires after 60 days and then it will cost $40 to register. This version allows you to view the extra info such as signal strength as well as the ability to do batch exporting of the text files (the export feature will expire, but the batch export feature, which is actually more useful, does not)
Generating text files
On the Web:
You can now generate a text file for your samples using the same web interface where you download your data:
1) Select the folder to be extracted.
2) Click on the "extract text from selected folder" bar.
3) Enter a file name.
4) You will get a FASTA format text display of every sequence in that folder.
5) This can be saved to a file (File->Save As…), or cut and pasted wherever you need it.
On the Mac:
To generate a text file from the capillary electropherogram in EditView, you have two choices:
1) Use the “Export as text” command from the file menu.
2) Click on the CATG button, in the lower left corner, then copy the text to the clip board, open simple text or some other text editor and paste the text.
To generate a text file in Traceviewer, select Export to FASTA from the file menu.
FinchTV does not currently support the exporting of text.
Generating Text Files on the PC:
Chromas Version 2.21) The fastest method is to choose File->Batch Export... Then navigate to the folder with your chromatograms, set Save as Type to Formatted Text, then click export.
Chromas Version 1.45) Open your chromatogram, choose File-> Export, select which folder you wish to save to, set Save as Type to Text, then click export.
Bioedit) Open your chromatogram, choose File-> Export as text, select which folder you wish to save to, type a filename for your text file , then click save.
Traceviewer) select Export to FASTA from the file menu.
FinchTV) does not currently support the exporting of text.
Computer Analysis Options
As a rule, we don’t provide free computer analysis for sequencing. See the “UWBC DNA Sequencing Prices” for analysis options on large projects. However, we will do limited assemblies of sequences for instructional or illustrative purposes. If you need further analysis, a number of commercial and freeware software packages are available to carry this out. Please remember that fragment analysis data will not be viewable with sequencing software. Contact us for the programs available for viewing fragment analysis data.
1) Dr. Dominik Hepperle has several software programs available at http://wwwuser.gwdg.de/~dhepper/software.htm
2)TIGR has a number of free programs at http://www.tigr.org/software/
3)GCG package homepage is at http://www.accelrys.com/products/gcg_wisconsin_package/
4)GCG access on campus can be found at http://www-biocomp.doit.wisc.edu/gcg.shtml
5)Gene Code Co. produces a popular comercial package called Sequencher at http://www.genecodes.com/
6)EMBOSS is a GCG freeware alternative: http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/
7)The Staden Package is at http://staden.sourceforge.net/
8)Some Mac freeware is available at http://web.tiscali.it/biologia/soft.htm
9)DNA Star lives at http://www.dnastar.com
10)The Phred/Phrap/Consed System Home Page is at http://www.phrap.org
Remember also the free BioEdit program described above for use on PC platforms.
For more sophisticated computer analysis contact Jean-Yves Sgro at firstname.lastname@example.org; for additional details on computer resources for biology also check out http://www.doit.wisc.edu/new_media_centers/
Finally, we have copies of articles that describe internet access to sequence databases for data comparisons, sequence alignment, and other functions. Just ask! It’s also worth just searching the internet—there are dozens of freeware utilities available to carry out a whole array of sequence analysis functions, just use your favorite search engine and you’ll often find what you need.