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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:

Filed under

The Scan

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.

Genome-Wide Analysis Sheds Light on Genetics of ADHD

A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.