Human gene sequence retrieval tool!

Overview of TFSearch Viewer:

Cis-regulatory elements can be enriched in the upstream sequences of a set of genes showing similar expression patterns, this can be done by searching for transcription factor binding sites(TFBSs) in the upstream sequences of the syn-expressed genes. TFSearch Viewer submit multiple sequences to TFSEARCH server automatically, it then searches for common TFBSs among search results of all sequences, providing evidence for co-regulation of the set of genes via transcription factors at the transcription level. The result file shows counts of each TFBS identified in each sequence, TFBSs are ranked by their occurence among all the sequences submitted, thus 100% ocurrence for a TFBS means the binding site can be detected in all the sequences.

Install TFSearch Viewer:

No installation required, it is downloaded as an executable jar file, just double click it, it will run.

System Requirements:

Both jar are tested on PC windows and Mac OS X, you will need jre1.3(java runtime environment) or jre1.4 installed in order to run the program. If you have jre1.3, you will be using tfsearch13.jar, if you have jre 1.4 installed, you will be using tfsearch14.jar. For PC, you can download and install jre from Sun Microsystems, Inc. at here.

For mac, from Finder->update software(or software update service), then it will bring up a page that have all the software available for download, find(or search) java 1.3 or 1.4, then update it. If you have Mac OS X, jre 1.3 should bundle with it, so you are all set.

Use TFSearch Viewer:

The GUI is very self-explantory, you will need to connect to internet to run the program, it is powered by TFSEARCH server(please go to the website for citation) and search engine by Yutaka Akiyama (Kyoto Univ.). You will need to put all you sequences into one file in FASTA format, all the result files will be saved in the same folder where your sequence file locates. Cautions:

Make sure your FASTA file in plain text format.
If you are using PC windows, .txt will work; if Mac OS X, texteditor mostly default as .rtf(rich text format), which will cause problem, because it is not flat text file, in the preference of texteditor, change the default to plain text, then it will work perfectly.
Files in the folder:
- youseq.txt: all sequences you have in fasta format, if you use EZRetrieve multiple retrieval tool retrieved your sequences, it will be All_Seq.FASTA, be sure to remove the first information line and the last information line in All_Seq.FASTA.
- seq.tmp: TFSearch Viewer program generated, which just concatenate sequences into one line.
- tfsearch.log: TFSearch Viewer program generated, contains errors if any, eg, duplicated sequences with same description lines.
- TFSearch.txt: TFSearch Viewer program generated, summary file of binding sites, tab delimited.
- seqname_TFSearch.html: TFSearch Viewer program generated, real TFSearch file saved on you computer, one for each sequence, so DO NOT put yourseq.txt on desktop if you have 1000 sequences, create a folder and put yourseq.txt in it.

Get TFSearch Viewer:
Download TFSearch Viewer!