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TCDB is operated by the Saier Lab Bioinformatics Group

Opensource Bioinformatics Tools

These programs are currently in use by the Saier Lab to analyze and establish homology in transport proteins.

These tools all require PHP5 & must be run on an educational network to have access to all features

  • DHDS - Distributed Homolog Detection System. This system uses multiple computers to collaboratively calculate statistical analyses between classes and families of proteins on a mass scale for the purpose of detecting new homologs. By V. S. Reddy & M. Saier, 2010.
  • Protocol1 - Automatically downloads a refined database of homologs from a single protein or accession number. Will use NCBI's BLAST to retrieve sequences & Make_Table5 to remove redundancies and abnormally long/short sequences and annotate sequences with conveneient symbols [Demo]. By V. S. Reddy & M. Saier, 2010.
  • Protocol2 - Compares two lists of FASTA sequences or one Clustal alignment file using the Smith Waterman algorithm to locate local alignments. Protocol2 will run GSAT on results with with 10 standard deviations (S.D) or higher. Protocol2 generates a detailed HTML report displaying each result sorted by its value in descending order along with GSAT score, local alignment, Needleman Wunsch global alignment and, total TMS. It can also display best aligning TMS regions [Demo]. By V. S. Reddy & M. Saier, 2010.
  • GSAT - Global Sequence Alignment Tool - Compares two sequences using the Needleman Wunsch alghorithm and determines the best alignment. The second protein is shuffled several times, depending on the protein sequence length and reports the comparison score expressed in deviations (S.D), based on how far the original NW score is away from the average NW score (Standard Score or "Z" Value). 10 S.Ds and up is considered worthy for establishing homology [Demo]. By V. S. Reddy & M. Saier, 2010.
  • TMSAlign - Preforms a ClustalW multiple alignment with a FASTA file or uses an existing alignment file to generate an HTML document displaying all annotated sequences with predicted TMS regions numbered and highlighted. Total predicted TMS regions are displayed at the end of the sequence [Demo]. By V. S. Reddy & M. Saier, 2010.
  • HMMGAP - This tool is used within other programs, and will take an input sequence & a segment of the same sequence containing gaps ("."), and returns the segment while maintaining gap spacings with annotated TMS regions numbered relative to the entire sequence. Uses HMMTOP for TMS predictions [Demo]. By V. S. Reddy & M. Saier, 2010
  • MPVT - Movable Protein Visualizer Tool - Requires two sequences and highlights the best local alignment, marks TMS regions and allows users to click and drag sequences to visualize different alignments [Demo]. By V. S. Reddy & M. Saier, 2010.
  • SortTree - Sorts any FASTA file or .TAB file according to any phylogenetic tree file (.PH) [Demo]. By V. S. Reddy & M. Saier, 2010.
  • ALN2FAS - Converts a ClustalX or ClustalW alignment file to a FASTA sequence & selects a range of residues one may wish to export [Demo]. By V. S. Reddy & M. Saier, 2010
  • GBLAST2 - Updated version of GBLAST. Runs a BLAST analysis on a selected genome file and returns a tab separated value sheet of transport proteins in TCDB with annotations and tabulated TMS data. This program retains the top hit for each TCID retrieved. By V. S. Reddy & M. Saier, 2010.
  • GenomeCompare - Compares a subject genome file to multiple target genomes simultaneously and identifies which sequences from which target organisms are most closely related to each subject sequence. By V. S. Reddy & M. Saier, 2010.

  • getNcbiSeq.pl - Downloads homologs from NCBI's NR database via blastp via commandline.

  • SuperTree.pl - Creates a super-family tree based on BLAST bitscores.