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