New/Updated Sequence Analysis/Linkage Programs on the Helix Systems (Helix)

We are pleased to announce the following new additions and updates of 
sequence analysis / linkage programs on the Helix Systems.

IPRScan, v4.3.1 installed 
[Biowulf] http://biowulf.nih.gov/apps/iprscan.html
InterProScan (IPRScan) is a tool that combines different protein 
signature recognition methods into one resource. IPRScan not only wraps 
the sequence analysis applications, it also extracts a considerable 
amount of information from the Interpro database, which integrates the 
PROSITE, PRINTS, Pfam, ProDom, SMART, TIGRFAMs, PIR superfamily, 
SUPERFAMILY, Gene3D and PANTHER databases. Each member database in IPR 
is used by different scanning applications that are combined in IPRScan.
IPRScan on Biowulf is designed to be used for bulk sequence analysis 
such as hundreds or thousands of sequences. 

ExPlain, v2.3 installed 
[Helixweb] https://helixweb.nih.gov/biobase/index.html
Available to all NIH users, the ExPlain Analysis System promotes biological 
interpretation of high throughput experiments like microarrays, proteomic 
data, and ChIP-chip experiments. The intuitive workflow allows systematic 
creation of experimentally testable hypothesis for both gene transcription 
regulation and signalling networks.

Fasta, updated to v35 
[Helix] http://helix.nih.gov/Applications/fasta.html
[Biowulf] http://biowulf.nih.gov/apps/fasta.html
The FASTA programs find regions of local or global (new) similarity 
between Protein or DNA sequences, either by searching Protein or DNA 
databases, or by identifying local duplications within a sequence. Other 
programs provide information on the statistical significance of an 
alignment. Like BLAST, FASTA can be used to infer functional and 
evolutionary relationships between sequences as well as help identify 
members of gene families.

Eigensoft, v2.0 installed 
[Helix] http://helix.nih.gov/Applications/eigensoft.html
The EIGENSOFT package combines functionality from population genetics 
methods and EIGENSTRAT stratification correction method.

Mega2, updated to v4.0_r1 
[Helix] http://helix.nih.gov/Applications/mega2.html
Mega stands for Manipulation Environment for Genetic Analysis. Mega2 is 
a data-handling program for facilitating genetic linkage and association 
analyzes.

Mendel, updated to version 8.0.1 
[Helix] http://helix.nih.gov/Applications/mendel.html
Mendel is a comprehensive package for exact statistical genetic analysis 
of qualitative and quantitative traits.

Merlin, updated to v1.1.2 
[Helix] http://helix.nih.gov/Applications/merlin.html
MERLIN uses sparse trees to represent gene flow in pedigrees and 
performs rapid haplotyping, genotype error detection and affected pair 
linkage analyzes.

Plink, 1.03 installed 
[Helix] http://helix.nih.gov/Applications/plink.html
PLINK is a free, open-source whole genome association analysis toolset, 
designed to perform a range of basic, large-scale analysis in a 
computationally efficient manner.

Relpair, 2.0.1 installed 
[Helix] http://helix.nih.gov/Applications/relpair.html
Relpair is a program that infers the relationships of pairs of 
individuals based on genetic marker data, either within families or 
across an entire sample.

Simlink, 4.12 installed 
[Helix] http://helix.nih.gov/Applications/simlink.html
Simlink is a program for estimating the power of a proposed linkage 
study by computer simulation.

Unphased, updated to 3.0.12 
[Helix] http://helix.nih.gov/Applications/unphased.html
UNPHASED is a suite of programs for association analysis of multilocus 
haplotypes from unphased genotype data. UNPHASED features.


Rosetta, updated to v2.3 
[Biowulf] http://biowulf.nih.gov/apps/Rosetta.html
Rosetta enables the prediction and design of protein structures, protein 
folding mechanisms, and protein-protein interactions.

Genome Browser Mirror Fragments Guinea Pig genome added 
[Helixweb] http://genome.cit.nih.gov
The Genome Browser supports text and sequence based searches that 
provide quick, precise access to any region of specific interest. 
Secondary links from individual entries within annotation tracks lead to 
sequence details and supplementary off-site databases.

Huygens Professional and Scripting, updated to v3.2 
[Helix] http://helix.nih.gov/Applications/huygens.html
The Huygens Suite is a complete and easy to use microscopic image 
restoration (deconvolution) package which uses an X-Windows GUI.



This message is being sent to all users of the Helix Systems. Important
announcements regarding our systems will be sent out occasionally. To
unsubscribe, click here, type your helix email address or your full name
in the message body and click 'send'. Please email listadm@helix.nih.gov
if you have any questions. 

Helix Systems, CIT, NIH, HHS