Molecular Biology Program Bioinformatics and Educational Resources - Bioinformatics Tools

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]

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]

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 top hits of these BLASTs may be sorted by in different ways, and Genbank and other database links for matched subject sequences are provided. [HELP]

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: 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: 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]

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