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X-Miner 1.0, Apollo, GenBank

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X-Mine has released two new products: X-Miner 1.0, a computational platform for genomic data mining that combines aspects of modern statistics, pattern recognition, and high-performance parallel computing; and X-Refiner 1.0, a searchable catalog of millions of database entries containing reports, annotations, comments, HTML, XML, images, and links to external data sources.

 

The Apollo genome browser, a collaborative project between the Berkeley Drosophila Genome Project and Ensembl, is now available through www.ensembl.org/apollo. Apollo was initiated as a fly genome annotation tool, but is also able to annotate and browse any large eukaryotic genome. The fly-specific Apollo annotation tool is available at www.fruitfly.org/ annot/ apollo.

 

GenBank release 125.0 is available via ftp from the National Center for Biotechnology Information at ftp.ncbi.nih.gov.

Release 125.0 contains 13,543,364,296 base pairs and 12,813,516 entries—up 0.570 billion base pairs and 569,750 sequence records from the June 124.0 release. The 125.0 flat files require approximately 49.72 GB for the sequence files only. The ASN.1 version requires approximately 45.06 GB.

 

Genops Bioinformatics has made a free evaluation version of its Ngene 1.07 integrated sequence analysis package available through its website, www.genops.com.

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The Scan

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.

TB Resistance Insights Gleaned From Genome Sequence, Antimicrobial Response Assays

Researchers in PLOS Biology explore M. tuberculosis resistance with a combination of sequencing and assays looking at the minimum inhibitory concentrations of 13 drugs.

Mendelian Disease Genes Prioritized Using Tissue-Specific Expression Clues

Mendelian gene candidates could be flagged for further functional analyses based on tissue-specific transcriptome and proteome profiles, a new Journal of Human Genetics paper says.

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.