Tools -- programs and software  




454 Replicate Filter
This tool clusters and filters out artificially replicated sequences in 454 data. It returns a fasta file of unique sequences and a list of the sequences in each cluster. Described in:
- Teal TK, Schmidt TM. Identifying and removing artificial replicates from 454 pyrosequencing data. Cold Spring Harb Protoc. Apr. 2010.
- Gomez-Alvarez V*, Teal TK*, Schmidt TM. Systematic artifacts in metagenomes from complex microbial communities. ISME J. 3(11): 1314-17 (2009)

A program for motif searching in genomes. Described in:
- Dietrich LEP, Teal TK, Price-Whelan A, Newman DK. Redox-active antibiotics control gene expression and community behavior in divergent bacteria. Science. Vol 321. no. 5893, pp.1203-1206. (2008)
- Teal TK, Studies of the Spatial Organization of Metabolism in Shewanella o\ neidensis and Pseudomonas aeruginosa Biofilms PhD Thesis, Computation and Neural Systems. California Institute of Technology. (2007)

A Python program to create oligos from a file of gene sequences

Developer for:

An information extracting and processing package for biological literature

A digital evolution research platform

  Last updated: April 12, 2012
Title photo credit: William R. Hewlett, California Academy of Sciences