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LARTS, InstaSeq, ArrayGenius OnDemand, go.biomind.com, International Protein Index, UniProt 5.0, Swiss-Prot 47.0, Trembl 30.0, Genome Reviews

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LifeFormulae is seeking beta testers for LARTS (LifeFormulae ASN.1 ReaderToolSet), software for mining data in NCBI's ASN.1 format. The software converts NCBI ASN.1 binary data to XML using the Java XMLFilter interface. Information on the beta-tester offer is available at http://www.lifeformulae.com.


InstaSeq, a software tool that uses the Google code to search for records relating to biological sequences, is available from Georgetown University at http://bioinformatics.georgetown.edu/InstaSeq.htm. The tool runs on a Java script above the Google search engine, and returns the associated links and documents.


Biomind has released two new web-based tools: ArrayGenius OnDemand, an online version of its ArrayGenius microarray data analysis product, and go.biomind.com, which uses machine-learning algorithms to predict the appropriate Gene Ontology categories for hundreds of previously unclassified human genes. With ArrayGenious OnDemand, Researchers can upload microarray data to http://ondemand.biomind.com/index.htm, and receive analysis results by e-mail. ArrayGenius OnDemand is currently free. After "an introductory period," the company said it will charge for certain aspects of the service. Biomind said that it will launch another online tool, called PathwayGenius OnDemand, later this year.


The European Bioinformatics Institute has released an updated version of the International Protein Index database at ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/. The database, compiled from Swiss-Prot, Trembl, RefSeq, and Ensembl, contains 49,923 entries for human, 42,802 for mouse, and 39,375 for rat.

EBI has also released UniProt 5.0, which includes Swiss-Prot 47.0 and Trembl 30.0. UniProt 5.0, available at http://www.ebi.uniprot.org/index.shtml, includes a total of 1,896,046 entries. Swiss-Prot 47.0 contains 181,571 sequence entries, comprising 65,742,349 amino acids abstracted from 128,438 references. Trembl 30.0 contains 1,714,475 sequence entries comprising 540,729,498 amino acids.

EBI has also released version 26 of Genome Reviews, a collection of curated versions of EMBL/GenBank/DDBJ database entries, at http://www.ebi.ac.uk/GenomeReviews/. The release includes 379 entries, 224 complete genomes, 710,588,291 nucleotides, and 659,717 protein-coding sequences.

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The Scan

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.

Analysis of Endogenous Parvoviral Elements Found Within Animal Genomes

Researchers at PLOS Biology have examined the coevolution of endogenous parvoviral elements and animal genomes to gain insight into using the viruses as gene therapy vectors.

Saliva Testing Can Reveal Mosaic CNVs Important in Intellectual Disability

An Australian team has compared the yield of chromosomal microarray testing of both blood and saliva samples for syndromic intellectual disability in the European Journal of Human Genetics.

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.