Software
EpDis
- EpDis is a tool for simultaneous access and visualization of different prediction methods, and combining and comparing results obtained by their application to the same input data. It is developed to facilitate research for biologists and immunologists.
EpDis can process protein sequences from different sources: FASTA files, RDBMS, Uniprot database or raw sequences. It supports execution of various T-Cell epitope predictors, disorder and disordered-binding predictors and hydropathy. EpDis tool is modular and configurable, easily extensible with additional predictors, implemented in Java.
ForiC
- ForiC is a cutting-edge web tool designed for the rapid and efficient prediction of oriC regions in bacterial genomes. Written in PHP, ForiC accepts input in FASTA format and outputs comprehensive analyses including GC, CGC, AT, and CAT skews, along with the prediction interval. Leveraging advanced GC and CGC skew methods, ForiC offers a significant improvement in computational efficiency, completing predictions in mere seconds. This user-friendly application is now publicly available for researchers to download and integrate into their workflows. Detailed instructions for installation, usage options, and test cases are provided to ensure seamless integration.
MassPred
- MassPred is a set of tools that provides easy predictor installation, application of predictors to input data and filtering of the results of predictor action.
MassPred takes the contents of input files or directories, extracts every single protein and applies the desired predictors to the extracted proteins, creating separate jobs that can be simultaneously executed on a symmetric multiprocessor computer, or on computers with a multicore/multithread processor architecture. MassPred itself does not perform a parallel execution of a single predictor application to a single protein.
PBsPredictors
- PBsPredictors is a group of models for the prediction of structural alphabet Protein Blocks
from the sequence information of a protein chain. Models were developed using different data
mining approaches and machine learning algorithms implemented in Python packages or available
in IBM SPSS Modeler. For the PBs prediction, models use amino acid sequence, indicators of repeat
appearances in a sequence, results of structural protein properties predictor, and results of different
predictors of protein intrinsically disordered regions.
RepeatsPlus
- RepeatsPlus is a set of programs that provides statistical filtering according to input sequence length and number of repeat occurrences, motif mask filtering and filtering related to ambiguous letters in input sequence and a large number of other options. RepeatsPlus package contains two batch-processing console programs StatRepeats and Repeats written in C++ and a graphical user interface RepeatPlus written in Python that simplifies execution one of the two console programs based on its options. The RepeatPlus package also contains two standalone batch-processing console programs MotifSearch (writen in C++) and DrawRepeats (written in C).
StatRepeats
- StatRepeats is a tool for finding maximal repeats in an input (nucleotide or protein) sequence. It can extract four types of repeats: direct non-complementary, direct complementary, inverse non-complementary and inverse complementary repeats. It can use statistical estimation to extract only statistically significant repeats, or all repeats. It also can filter the set of found repeats based on the specified p-value.
Results can be redirected to the standard output, to files in a few different formats, or directly into an ODBC-compatible database.
