Archive for the ‘Software’ Category

Official BioV Documentatin

The link to the BioV Webpage is http://biov.tcdb.org/

To view documentation on all BioV tools, click this link:

To read the paper by Reddy & Saier, 2012, describing in detail how each program works, click here

Super Family Tree (SFT) Program

Download and Installation:

The SFT programs can be downloaded from the Lab-Software section of the Transporter Classification Database (TCDB; www.tcdb.org) website.  These programs will require a MacOS computer with BLAST programs (psiblast, blastcl3, blastall, etc) and cd-hit installed.  The programs, getNcbiSeq.pl and supertree.pl, should be downloaded and placed into your bin folder.  You will need to change the permissions of these programs using the chmod command as necessary.  Then the programs, fitch and consense, should be downloaded and installed using the ProtPars software package (http://evolution.genetics.washington.edu/phylip/doc/protpars.html).  The older version of the Tree View (TV) program can be downloaded from the Biotools section of TCDB or http://taxonomy.zoology.gla.ac.uk/rod/treeview.html or the newer versions can be downloaded from http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download.html.

Second Section (insert between sections “Step 6: SFT2A and SFT2B” and the last section containing the citations):

Experiencing difficulties?

For assistance with these programs:

e-mail: jchen@alumni.ucsd.edu

Please include with your request

(1)  name

(2)  lab

(3)  current project

(4)  contact info (phone number and email)

(5)  location of your files

(6)  the exact nature of your problem

Response times will vary between 1-3 days.  I will do my best to respond and resolve issues promptly. Thanks.

 

Find out highlighted TMS regions in the sequence using HMMGAP

HMMGAP is a tool that is used within several other programs and can also be used as a standalone feature. HMMGAP takes two parameters: “Input Sequence” and “Gap Segment.” Gap Segment refers a segment of the input sequence containing gaps delimited with periods. HMMGAP returns the segment with highlighted putative TMS regions that are numbered relative to the entire sequence. The input segment does not have to contain gaps, but is usually determined by a Needleman Wunsch comparison.

HMMGAP can be accessed online here

To access the standalone version, type the following syntax in the terminal window

Read more

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