Seqool - A sequence analysis tool
Signal search, pattern recognition, and sequence
Seqool is a free (for educational use) sequence analysis
software designed primarily for searching biological signals
in nucleic acid sequences. The sequence analysis program package provides several
pattern recognition models, but it also includes the most common sequence
analysis statistics, such as GC content, codon usage, etc.
The Seqool sequence analysis software offers several pattern recognition
methods for searching for biological signals, such as splice sites or user
specific signals. Pattern recognition models include weight
matrices (profiles), position specific score matrices, binding energy
based signal search models (e.g. for snRNAs), maximum dependence decomposition
models, profile hidden Markov models, and models scorring the composition of a sequence.
Models can be combined using e.g. decision trees or neural networks
in order to construct more refined models or for combining information
from several models or sequence statistcs for a final classification
of a signal.
The Seqool sequence analysis tool also includes text search algorithms for the
identification of simple signals. The support of IUPAC nucleic acid codes (such
as ‘y’ for pyrimidines) allows less strict text searches. Over-represented
oligonucleotides ("words") can be identified and optionally clustered
to groups of similar words. Additional features of the sequence analysis software
include the calculation of sequence composition statistics (GC, codon usage,
nucleotide and oligonucleotide frequencies) and a manipulation and extraction
tool for sequence or text-files.
The main features of the Seqool sequence analysis program package
Basic sequence analysis:
Nucleotide composition, oligo-nucleotide
GC content, codon usage, codon preference
Calculation of over- or under-represented
Calculation within windows of a given size
or for whole sequences, for single sequences or several sequences
Extraction of sequences with a given composition
(e.g. sequences with a GC content lower than 0.41)
Exact text search, text search using IUPAC
codes (e.g. "y" for pyrimidines), search of repeats, stop
and start codons, restriction sites
Profiles (weight matrices/position specific
Profile hidden Markov models
Maximum dependence decomposition
Oligo-nucleotide frequency models / models
for sequence composition (e.g. GC, codon usage, codon preference,
frequencies of nucleotides or oligo-nucleotides)
Search for RNA binding motifs (based on binding
energy, e.g. snRNPs)
Neural networks (Backpropagation networks)
Model combinations by addition or subtraction
of scores (Hybrid models)
Models scoring the distance between signals
Support of the most common sequence file formats,
such as FastA, GenBank, GCG, EMBL, and plain sequences (raw).
A comprehensive sequence and text formatation
and extraction tool (FastAFormat) which allows the extraction
of sequences from virtually any file format.
Download the sequence analysis software Seqool
• Manual • Download
BIOSSC/Seqool is not responsible for the content of external links.
Last Changes 24.02.2007