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Bioinformatics


SWBIC Products & Services >> Bioinformatics

Tools

PCAPSS PCAPSS (Protein Classification through the Assessment of Predicted Secondary Structure): A new fold-recognition tool for helping identify hypothetical protein sequences. From a single query protein sequence, it builds a hidden Markov model of predicted secondary structure to search the PDB for proteins of similar structure. [HELP]

Blast Filter BLAST Filter: Builds a set of related sequences by running BLAST on your DNA or protein query sequence, filtering the matches through a set of rules, and returning the complete sequences of the BLAST matches that pass all rules. Includes user-defined rules and a graphical display of High Scoring Segment Pairs aligned with the query. Useful in building a sequence set for multiple alignment, phylogeny, and hidden Markov models. [HELP]

Batch BLAST Batch BLAST: A service provided by SWBIC to the NMSU research community. It runs the Basic Local Alignment Search Tool (BLAST) for many query sequences. The results of these BLASTs may be sorted by the queries that resulted in the most significant matches to database sequences. Graphical alignment of High Scoring Segment Pairs is also provided, as well Genbank links for matched subject sequences. [HELP]

Graph Align GraphAlign: Performs a new type of graphical analysis of global pairwise alignments between a query sequence and multiple subject sequences. It provides new methods for analyzing and visualizing how a query (protein, DNA or RNA) aligns with a set of related sequences. [HELP]

TransForm TransForm: Translates and validates data files used by multiple alignment and phylogenetics programs. Currently, TransForm performs the following: translates NEXUS format to PHYLIP format, translates PHYLIP format to NEXUS format, and validates that NEXUS files are properly formatted . [HELP]

SeqCheck SeqCheck: Provides several utilities for formatting and analyzing a file of one or more sequences, including line formatting, alphabet checker, and composition analysis. [HELP]

SeqMake SeqMake: Generates up to 10,000 random DNA, RNA, protein or user-defined sequences. Sequences can be generated from an input sequence by shuffling or generated from standard or user-defined compositional frequencies. Sequence lengths can also be randomized in several ways. [HELP]

SeqEST SeqEST: Prepares an NCBI dbEST sequence submission file based on a user-supplied file of sequences. A time-saver when preparing dbEST submission files that also assures that all obligatory fields are provided. [HELP]

EnViruSAT EnViruSAT (Enteric Virus Sequence Analysis Tools): Dedicated to the acquisition and analysis of viral genomes of enteric viruses. It provides the means for researchers and students to rapidly collect citations or nucleic acid and amino acid sequence information for these viruses and analyze the information on selected web-based software to suit the researcher's needs.

EXTNUM EXTNUM (EXTended NUMeric): A C++ class implementation that provides the user with a floating point number type that extends the dynamic range (i.e., the allowable range of the exponent) for a double type floating point number, while preserving the approximate 15 digit precision of the double as well. It is useful in Bioinformatics software that works with large exponents.

Databases

PathDB PathDB: A Metabolic Pathway Database developed by the National Center for Genome Resources (NCGR) and funded in part by SWBIC.

 

 
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