Welcome to Pen

The Portuguese EMBnet Node is installed at the

Instituto Gulbenkian de Ciência

Apartado 14

2781-901 Oeiras

Portugal

Node Description

The Portuguese node of the EMBnet is run by the Bioinformatics Unit of the Instituto Gulbenkian de Ciência and delivers to its 200 users a service that consists of providing access to periodically updated copies of about 20 databases of sequence data, a suite of correctly installed and documented programs to process sequence data and user support via e-mail or telephone. Most of these services require the use of an individual account in our server. To obtain such an account you must register with our biocomputing services.

Packages and Databases

 General Sequence Analysis Packages

• GCG - v. 10.0 Genetics Computer Group Inc. (Wisconsin package) user´s manual
• EMBOSS - European Molecular Biology Open Software Suite documentation
• STADEN - v. 2001 user´s manual
• READSEQ - Sequence format conversion documentation

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Multiple Sequence Analysis

• Clustal W v. 1.8 documentation
• Clustal X v. 1.8 Graphical sequence alignment user´s manual

Phylogeny and Evolution

• PHYLIP - v. 3.5c Package for inferring phylogenies user´s manual
• PUZZLE - v. 4.0 - Program for reconstructing tree topologies with quartet puzzling user´s manual
• PAUP - Analysis using parsimony - provided via GCG v. 10.0 user´s manual
• MOLPHY -  v. 2.3b3 - ProtML, NucML and NJDist phylogeny programs documentation

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Genetic Analysis

• ANALYZE - Accessory programs to the Linkage package documentation
• APM - Affected Pedigree-Member Method documentation
• ASPEX - set of programs for performing multipoint exclusion mapping of affected sibling pair data for discrete traits documentation
• FASTLINK - Fast versions of the original Linkage documentation
• GAS - Genetic Analysis System documentation
• GENEHUNTER - Multipoint analysis of pedigree data user´s manual
• LINKAGE - General linkage package user´s guide
• MAPMAKER/EXP - Constructing Genetic Linkage Maps documentation
• QTDT - Quantitative (Trait) Transmission/Disequilibrium Test documentation
• QTL Cartographer - Mapping quantitative trait loci onto a genetic linkage map documentation
• SimIBD - Simulation programs for IBD documentation
• SOLAR - Package for genetic variance components analysis  userīs guide 
• TLINKAGE - Two locus trait linkage programs documentation
• X-LINKED APM - X-linked version of the APM programs

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Searching for databases

• SRS a Sequence Retrieval System at  EBI
• Entrez  a retrieval system for searching several linked databases at NCBI

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Unixhelp by John Smith (v7.0)

Key Contacts:

Node manager:
Pedro Fernandes
E-mail: pfern@igc.gulbenkian.pt
Telephone: +351 214407912

Bioinformatics User Support:
Isabel Marques
E-mail: imarques@igc.gulbenkian.pt
Telephone: +351 214407914

Address:

Rua da Quinta Grande 6, 2780-156 OEIRAS, PORTUGAL
Apartado 14, 2781-901 OEIRAS, PORTUGAL
Telephone: +351 214407900
Fax: +351 214407970

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