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Peaks, dbSNP, BioRuby 0.3.7, Protein Data Bank, Journal of Biology


Bioinformatic Solutions of Waterloo, Ontario, Canada, has released Peaks, software for the identification of protein peptides from mass spectrometry data. According to the company, the Peaks algorithm searches for the best possible peptide matches based on a scoring scheme, automatically detects many posttranslational modifications, including phosphorylation, and is able to detect peptides that are not found using database search software.


Build 105 of the dbSNP database is now available from the National Center for Biotechnology Information at ftp://ftp.ncbi.nlm. New content since build 104 was released in May includes 6,644 new human submissions, 44,491 RefSNP clusters for human, and 26,667 RefSNP clusters for mouse.


Toshiaki Katayama of the Bioinformatics Center at Kyoto University’s Institute for Chemical Research has released BioRuby 0.3.7 at: New features include API unification and modularized servers and formats.


The Macromolecular Structure Database group at the European Bioinformatics Institute has added several new services to the Protein Data Bank, including Secondary Structure Matching, a tool for protein structure comparison (at and the Hetgroup interface for accessing the MSD’s reference data warehouse of ligands and small molecules (at


The Journal of Biology posted its inaugural issue online last week ( The peer-reviewed journal provides immediate free access to articles and allows authors to retain copyright of their work. The journal’s publisher, BioMedCentral, said it plans to publish articles of the same quality as those in Science, Nature, and Cell. Martin Raff is the editor of the journal, and several scientists who launched the Public Library of Science initiative early in 2001 sit on the editorial board.


Filed under

The Scan

Pig Organ Transplants Considered

The Wall Street Journal reports that the US Food and Drug Administration may soon allow clinical trials that involve transplanting pig organs into humans.

'Poo-Bank' Proposal

Harvard Medical School researchers suggest people should bank stool samples when they are young to transplant when they later develop age-related diseases.

Spurred to Develop Again

New Scientist reports that researchers may have uncovered why about 60 percent of in vitro fertilization embryos stop developing.

Science Papers Examine Breast Milk Cell Populations, Cerebral Cortex Cellular Diversity, Micronesia Population History

In Science this week: unique cell populations found within breast milk, 100 transcriptionally distinct cell populations uncovered in the cerebral cortex, and more.