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Aldente, Protcomp 6.0, Finch on Sun, RefSeq 7, GenePlot, STRAP, Wrappers4EMBOSS

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The Swiss Institute of Bioinformatics has added a new tool called Aldente to its ExPasy suite of protein identification and characterization tools. The software, available at http://www.expasy.org/tools/aldente/, identifies proteins from peptide mass fingerprinting data using the Hough transform to determine the mass spectrometer deviation, to realign the experimental masses and to exclude outliers. The Aldente algorithms are also included in the Phenyx software platform from Geneva Bioinformatics (http://www.phenyx-ms.com/).


Protcomp 6.0, a program for predicting the subcellular localization of eukaryotic proteins, is available from Softberry at http://www.softberry.com/berry.phtml?topic=protcompan&group=programs&subgroup=proloc. The company said that the software has an overall prediction accuracy of greater than 90 percent.


Geospiza and Sun Microsystems have partnered to offer Finch on Sun — an out-of-the-box installation of Geospiza’s Finch sequence data management software running on Sun’s V20z Opteron server. The companies said they are providing the server free for a limited time. Further information is available at www.geospiza.com/sun.


RefSeq 7 is available from the National Center for Biotechnology Information at ftp://ftp.ncbi.nih.gov/refseq/release/. This release incorporates genomic, transcript, and protein data available as of Sept. 12, and includes 1,144,638 proteins and sequences from 2,558 different organisms.


NCBI has also released a new pair-wise comparison tool called GenePlot at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome. GenePlot can be used to visualize similarities between bacterial genomes and is available for selected microbial reference genome records in Entrez Genome.


STRAP (Structural Alignment Program) is available from Humbolt University at http://www.charite.de/bioinf/strap/. The program is an interactive, extendable and scriptable editor for large protein alignments, and it integrates amino acid sequences, secondary structure, 3D structure and genomic and mRNA sequences. STRAP is written in Java and runs on Windows, Mac OS X, Unix, and Linux.


Version 1.0 of Wrappers4EMBOSS is available at http://www.wemboss.org/Folder.2003-09-11.4050/Folder.2003-09-11.4318C/wrappers4EMBOSS-1.0.tar.gz. Wrappers4EMBOSS provides EMBOSS interfaces for Fasta, Blast, Clustal, bscan, psscan, and pfmake, and was jointlyby the Argentinian and Belgian EMBnet nodes.

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The Scan

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.

Team Presents Cattle Genotype-Tissue Expression Atlas

Using RNA sequences representing thousands of cattle samples, researchers looked at relationships between cattle genotype and tissue expression in Nature Genetics.

Researchers Map Recombination in Khoe-San Population

With whole-genome sequences for dozens of individuals from the Nama population, researchers saw in Genome Biology fine-scale recombination patterns that clustered outside of other populations.

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.