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BioInform s Surfing Report: Web-Based Tools at Computational Genomics


Argo, from the Broad Institute, is a tool for visualizing and manually annotating whole genomes:

BOX-C (Blast Organism Cross-Comparison), from Hiram College, is a sequence gap closure method that aligns contigs through comparison to the NCBI non-redundant database:

Chisel, from Argonne National Laboratory, clusters protein sequences that are closely related in terms of homology and function:

MaGe (Magnifying Genomes), from Genoscope, is a software system for computational and manual microbial genome annotation:

MANATEE (Manual Annotation Tool, Etc., Etc.), from TIGR, genome annotation tool that can view, modify, and store annotation for prokaryotic and eukaryotic genomes:

PASA (Program to Assemble Sliced Alignments), from TIGR, is an automated system for genome annotation:

Pathema, from TIGR, is a pathogen database funded by the NIAID’s BRC program:

Picky, from Iowa State University, is an oligo microarray design program that identifies probes that are unique and specific to input sequences:

Puma2, from Argonne National Laboratory, is an updated version of ANL’s Puma database and bioinformatics suite for comparative analysis of genomes and metabolic networks (still in beta):

SNP-PHAGE (Single Nucleotide Polymorphism Discovery Pipeline for Haplotype Analysis and Genbank Submissions), from USDA, is a tool for polymorphism discovery:

WebGestalt, from Oak Ridge National Laboratory, is a genomic analysis toolkit that incorporates information from different public resources:

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The Scan

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