seq

Peter A Noble - Professor of Microbiology

Software Programs

Chaos Gene Representation

Chop up a gene sequence for Chaos Gene Representation (CGR) determination [Readme][Source code][test fasta file][output file you should get by running software]

Convert gene sequence into x- and y- coordinates [Readme][Source code][test fasta file][output file you should get by running software]

Count sequences within CGR boxes using x- and y- coordinates [Readme][Source code][test fasta file][output file you should get by running software]

Count sequences around a specific target (e.g., AGT) in a CGR plot [Readme][Source code][test fasta file][output file you should get by running software]

Manipulate fasta files

Convert fasta files to one line files and remove verbose text [Readme][Source code][test fasta file][output file you should get by running software]

Insert sequence length and convert one-line sequence files to fasta format [Readme][Source code][test file][output file you should get by running software]

Determine the GC content of a DNA sequencing run [Readme][Source code][test file][output file you should get by running software]

Determine the GC content of each sequence in a DNA sequencing run [Readme][Source code][test file][output file you should get by running software]

Make a GC histogram of a sequencing run [Readme][Source code][test file][output file you should get by running software]

Calculate hexanucleotide frequencies and determine co-occurring sequences in a metagenomic sample

Determine hexanucleotide frequences for a metagenomic sample [Readme][Source code][test file][hexamer file][output file you should get by running software]

Determine the co-occurrence of sequences in a 454 sample [Readme][Source code][test file][output file you should get by running software]

Create a Blast database and query with fasta files

How to make a NCBI blast database [Readme][test file]

How to query a NCBI database with a fasta file [Readme][test file][output file you should get by running software][output file with header]

Purge Blast output by Percent Similarity and Minimum Alignment Length [Readme][Source code][test file][output file you should get by running software]

Determine the coefficients of an equation using matrix algebra

Overview [Readme]

How to compile the source code and example test and output files [Readme][Source code][matrix_h][Input file #1][Input file #2][output file you should get by running software]

Calibrate a DNA microarray and test the calibration with real data

Fast-track Overview [short version][long version]

Average probe signal intensities [Readme][Source code][input_1 file][input_2 file][input_3 file][input_4 file][input_5 file][input_6 file][output file you should get by running software]

Calibrate probe signal intensities [Readme][Source code][input_1 file][output file you should get by running software]

Calculate concentrations from intensities and calibrations [Readme][Source code][input_1 file][expt_test file][output file you should get by running software]