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MOST USED PubMed Google SRS-EBI translator-ya.com (..) english->spanish spanish->english Paulino-directlinks

Federico Abascal Protein Design Group - CNB - UAM fabascal@cnb.uam.es

Want to do recursive sequence searches and cluster the results to detect false positives, to asses remote homology relationships, to analyze the evolutionary history of a protein family, ...? Try the recursive-blast and Ncut-clustering server.

What's genetic engineering for (an introduction)?
 

Sequence Alignments Blast EMBL, NCBI (2 seqs), EBI PSI-Blast NCBI Bioccelerator (S&W) Sam - HMM Align 2 sequences S&W Clustal EBI AQUA(Alignment QUality Assessment) Sequence features TMHMM, TMpred, all COILS, Paircoil, Multicoil SignalP, Sigcleave.pm, ExPASy - Tools, PattinProt Protein Families PROTOMAP (old) SYSTERS PFAM COGs: orthologues&paralogues CluS+Tr

GeneFinding MetaGene GeneMark ORF Finder PROCRUSTES geneid tRNAscan-SE Genomes Genomes at NCBI: bacteria, human (NHGRI), Drosophila melanogaster. Genome Protemics (EBI) CUBIC: genome analysis and descr.    s      s  Other GeneQuiz Coils RDB

Programming Many tutorials(from www.cs.huji.ac.il) Perl Perl Quick Reference Perl Reference search.cpan.org Java Java tutorial from Sun Java Reference (1.1.6) index Other HTML, more PostgreSQL Latex, more XML intro (en español) netlib - math algorithms Meschach tut, and others

Browsers / links

SRS-EMBL	CNB library (search)	Infoseek
SRS-EBI	PubMed & Cubby	FAST FTP Search v4.0
SRS-INFOBIOGEN	SeqAnalRef	Yahoo
SRS-CNB	UAM library	Google
Pise-CNB	BioMedNet	BioHunt
	Pedro's BioMolecular Research Tools	Infotrieve - Free Medline
PDBsum	EBI's BioCatalog	CalPhotos
OCA	EBI's Software rep.

• Course on Computational Molecular Biology at WUSTL
• Introduction to Alignment Scoring Statistics (WUSTL)
• General course on Bioinformatics (UAM, Paulino Gómez Puertas)
• Pedestrian guide to analysing sequence databases (B.Rost and R.Schneider)
• Swiss-PdbViewer manual (expasy); another one (simpler) by Gale Rhodes
• Crystallography Made Crystal Clear (CMCC): Crystallography, NMR, Homology Modeling, Electron density maps, ....
• Rasmol tutorial by Gale Rhodes
• Rasmol manual by Roger Sayle
• Information about protein families (ProWeb Project)
• Tutorials from KEGG: pathways maps, genome maps, global function, ...
• ergito/genes.net's GENES online, famous experiments, cell biology, molecular biology
• Principles of Protein Structure, Comparative Protein Modelling and Visualisation at ExPASy (N.Guex and M.C. Peitsch)
• FSSP - help
• Protein structure prediction (an introduction, by Harry Mangalam).
• NCBI education
• BioComputing Hypertext Coursebook about alignments, substitution matrices, algorithms, phylogenetics, etc
• Multiple tutorials on Unix, GCG, Seqlab & Staden Tutorials from the University of Oxford
• Introto Statistics of similarity scores (NCBI)
• Course Statistics for the life sciences (Department of Statistics and Mathematics, Simon Fraser University)
• Courses of the EMBL sequence analysis service
• Glossary of genetic terms.
• David Gilbert courses. Introduction to bioinformatics (protein topology).
• Tutorial on Protein Alignments (sequence and structural ones; Mark Gerstein, Yale MB&B)
• Algorithms in Molecular Biology (Ron Shamir , Tel Aviv University Department of Computer Science)
• Graph algorithms good course about NP optimization problems.
• GCG manual (CNB); Wisconsin
• Links to a lot of courses and tutorials (CCP11 project - The Bioinformatics resource).
• More links (from Infobiogen).
• And more...  (from Ron Shamir , Tel Aviv University)
• Gene Finding Review by David Haussler
• EMBnet/CNB Computing Library
• Principal component analysis
• Pfam statistics (Bayesian model, bit scores, extreme value distr., etc)
• HMMER package documentation (from Dr. Sean Eddy, WUSTL; local copy)
• Graph algorithms applet (very pretty!!), RIOT, Dorit S.Hochbaum and Dr Olivier Goldschmidt.

Mathematics The Stony Brook Algorithm Repository StadHelp  (help with biostatistics, in spanish) Bioestadística (uma) netlib - math algorithms Principal component analysis Course Statistics for the life sciences (Simon Fraser University) Search for mathematics topics Mathematical Atlas: A gateway to Mathematics Eric Weisstein's World of Mathematics Mathematica Elementary Linear Algebra (Keith Matthews) Linear Algebra (Jim Hefferon) linear + algebra google's search

Language - Encyclopedias - Dictionaries - Online books Español La Página del Idioma Español Diccionario de la RAE Diccionarios, sinónimos, dudas, etc; Acentos-reglas Diccionario de burradas Diccionarios Anaya LINKS!! Encyclopedia Enciclopedias (from EL PAIS) Encyclopedia Britannica Translators e-lingo, babelfish, go translator, traductor-ya	Newspapers EL PAIS La Vanguardia El Mundo MiCanoa.com larazon Estrella Digital   Internet tools MailAndNews Sauce hotmail freenewsland.com Mixmail Bigfoot
Biology GENES online Cell and molecular biology dictionary Virtual Biology Kimball's Biology Pages Special Interest Groups at NIH Virtual Library: Biosciences, Computer science, etc Cell and Mol. Biol online	A Level Biology Human Phisiology The Biology Project A Molecular Biology Notebook MIT's Biology Hypertextbook Glossary of genetic terms Glossary of Biochemistry and Molecular Biology.

Science Divulgation Under construction www.sciencedaily.com www.explorezone.com www.100cia.com www.divulcat.com www.astrored.com www.bioplanet.net

Madrid Some interesting places: i.-  Museo del Prado ii.- Tyssen-Bornemisza Museum iii.- Plaza Mayor(more) iv.-Palacio Real v.- Jardín Botánico vi.-Parque del Retiro vii- Museo Reina Sofía Useful links to live Madrid: Madrid's map MuniMadrid METRO Guía del Ocio Madrid a mano 5 days in Madrid guide Madrid cinema's program (vamos, la cartelera) Cartelera y TV de EL PAIS Cinentradas (venta electrónica) Comunidad de Madrid AboutMadrid

Personal I'm working at the CNB Protein Design Group (see some people of the group feeding them selves, here) since January 1999, doing my thesis with a fellowship from Comunidad de Madrid since October 1999 (thanks!). I'm working in automatic function prediction in the context of genomic biology in collaboration with José María Fernández.You can find us here. Go here if you want to know more about my interests at Bioinformatics and/or Computational Biology. If you want to comment something with me, please do it (email).

Publications

• Here you can find the poster I presented at the "Structural Genomics and Bioinformatics" workshop in the Juan March Institute (March 2001).
• An article published at CNN+ online can be found here. (or a local version here, in spanish)
• And here, the poster that José María and me presented at "II Jornadas de Bioinformática", (Malaga, May 2001)
• Clustering of proximal sequence space for the identification of protein families.
Federico Abascal and Alfonso Valencia
Bioinformatics 2002;18:908-921.
(suplementary material)
• Reductive genome evolution in Buchnera aphidicola.
Van Ham RC, Kamerbeek J, Palacios C, Rausell C, Abascal F, Bastolla U, Fernandez JM, Jimenez L, Postigo M, Silva  J, Tamames J, Viguera E, Latorre A, Valencia A, Moran F, Moya A.
Proc Natl Acad Sci U S A. 2003;100:581-586
(project web-site)
• Automatic annotation of protein function based on family identification.
Federico Abascal and Alfonso Valencia.
Proteins. 2003; 50:683-692.
(suplementary material)
• Mi tesis: Análisis de genomas. Métodos para la predicción y anotación de la función de las proteínas. (septiembre 2003)
PDF: portada y agradecimientos, contenido.
PS: portada y agradecimientos, contenido.

 
 

• UCM - Escuela de verano 2003: Análisis de Secuencias.
• Alineamiento de secuencias. Búsqueda de parecidos. Alineamientos múltiples.
• Motivos y perfiles. Dominios. Familias de Proteínas.
• Máster de Bioinformática 2003: Análisis de secuencias. Patrones, perfiles, dominios y familias de proteínas.
• Patrones, perfiles y dominios.
• Más sobre patrones y perfiles: PSI-BLAST y HMMer.
• Familias de proteínas.
• UAM - curso de doctorado 2003: Análisis de secuencias: Búsqueda de homólogos con BLAST y PSI-BLAST.
• UAM - curso de doctorado 2002: El papel de las familias de proteínas en el análisis de secuencias.
• UCM - Escuela de verano 2002: Familias de Proteínas.

Contact information: Federico Abascal Protein Design Group, CNB-CSIC Cantoblanco Madrid 28049 Spain phone +34 91 585 46 69  fax: +34 91 585 45 06 email: fabascal@cnb.uam.es http://www.pdg.cnb.uam.es/fabascal UAM map       Wolves photos by Gerald and Buff Corsi. Copyright © 2001 California Academy of Sciences. Moon photos from NASA website. Other photos: National Geographic, Corbis, ??etc??(sorry)

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BioBooks - Bio Centers - Bio Tutorials- Browsers - Databases - Dictionaries - Español - Genomes - Interests - Journals - Links-pages - Madrid   - mail/news - Mathematics - Newspapers - People - Personal - Publications