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http://sbc.su.se/
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Stockholm Bioinformatics Center | sbc.su.se Reviews
https://sbc.su.se
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PrIME: Probabilistic Integrated Models of Evolution
PrIME, an acronym for Pr. Volution, is a library and accompanying tools for phylogenetics. PrIME mainly relies on Markov-chain Monte Carlo (MCMC) framework and probabilistic modeling. For announcements and discussion, subscribe to the PrIME users' mailing list. Note: Ignore the certificate warning!
Phobius
A combined transmembrane topology and signal peptide predictor. Paste your protein sequence here in Fasta format:. Select the sequence file you wish to use.
msa.sbc.su.se
Welcome to msa.sbc.su.se. A fast and accurate multiple sequence alignment algorithm:. An lightweight viewer for multiple sequence alignments and phylogenetic trees:. A program to assess the quality of multiple sequence alignments:.
jSquid Home
JSquid is a Java-Applet used for displaying FunCoup. Result graphs. It is based on Medusa. But offers several new features to explore and manipulate the graph. The program is published under the GPLv3. Therefore it is free of charge and can be used and modified by anyone according to the license's policy. JSquid has been published in Bioinformatics. The tutorial for creating XML input files has been added. 2007 · Klammer and Roopra ·.
Inparanoid
InParanoid: ortholog groups with inparalogs. 273 organisms: 3718323 sequences. Version 8.0, Updated December 2013 ( release notes. Select two species and view all their orthologs. SEARCH BY SEQUENCE IDs. View orthologs of a specific gene or protein. Query InParanoid by keywords. Find orthologs in InParanoid similar to your protein sequence. Obtain tables, html, orthoXML. Sequences and core data. Statistics of the database and genomes used. InParanoid Version 4.1 is available here.
Networks of functional couplings/associations - FunCoup
Search for functional couplings. Functional coupling, or functional association, is an unspecific form of association that encompasses direct physical interaction but also more general types of direct or indirect interaction like regulatory interaction or participation the same process or pathway. To search for genes coupled to your genes of interest or for couplings between them enter your genes in the text box and hit the search button. Supported identifier types for the search are:. A set of genes.
Excap
FunCoup
Members of the same complex. Which gene/protein IDs to use? Glycolysis / Gluconeogenesis, KEGG00010. Citrate cycle (TCA cycle), KEGG00020. Pentose phosphate pathway, KEGG00030. Pentose and glucuronate interconversions, KEGG00040. Fructose and mannose metabolism, KEGG00051. Galactose metabolism, KEGG00052. Ascorbate and aldarate metabolism, KEGG00053. Starch and sucrose metabolism, KEGG00500. Amino sugar and nucleotide sugar metabolism, KEGG00520. Pyruvate metabolism, KEGG00620. ATP synthesis, KEGG00193.
GPCRHMM
A GPCR detection method. Paste your protein sequence here in Fasta format:. Select the sequence file you wish to use. Run local score (Recommended).
Sonnhammer Bioinformatics Group
Erik Sonnhammer, Ph.D. DBB, Stockholm University. Science for Life Laboratory. Box 1031, SE-17121 Solna, Sweden. Email: Erik.Sonnhammer at scilifelab.se.
sbc.su.se
How to find SBC
http://www.sbc.su.se/map
SBC is located at SciLifeLab Stockholm ( map. Science for Life Laboratory. Tomtebodavägen 23A, Solna. Science for Life Laboratory. Science for Life Laboratory.
SBC Publications
http://www.sbc.su.se/publications
Schibich, D., Gloge, F., Pohner, I., Bjorkholm, P., Wade, R.C., von Heijne, G., Bukau, B. and Kramer, G. (2016) Global profiling of SRP interaction with nascent polypeptides. Nature. Rodriguez, D., Chakraborty, S., Warnick, E., Crane, S., Gao, Z.G., O'Connor, R., Jacobson, K.A. and Carlsson, J. (Epub 2016) Structure-Based Screening of Uncharted Chemical Space for Atypical Adenosine Receptor Agonists. ACS Chem Biol (Epub ahead of print). Heusser, S.A., Yoluk, O., Klement, G., Riederer, E&#...Soderstrom, B...
SBC
http://www.sbc.su.se/services
Services that are marked with * are not hosted at SBC but were developed fully or partly by people at SBC. Calculate trees from multiple alignments. Consensus fold recognition and meta server with homology modelling. A threading method for membrane proteins. A fold recognition server. A protein model quality predictor. A combined transmembrane topology and signal peptide predictor. Predicting the distance to the membrane center for residues in alpha-helical membrane proteins. Prediction of signal peptides.
User guide at SBC
http://www.sbc.su.se/user-guide/output/user-guide.html.utf8
User guide at SBC. 2 New computer users. 21 Applying for a new user account. 22 The first day you arrive. 23 When you log in for the first time. 231 Adjust your /.bashrc and /.bash profile. 232 Adjust your /.ssh/config. 233 Set thunderbird as your preferred mail client. 234 Set "Visual effects" to "None" in gnome-appearance-properties. 235 Get informed about the support policies. 31 Clean your work place. 32 Don't leave things at the office. 33 Organize your computer account. 41 SciLifeLab Policy Document.
SBC
http://www.sbc.su.se/courses
Comparative Genomics, KB8007, 7.5 ECTS. Applied Bioinformatics, DD2397, 7.5 ECTS at KTH. Introduces elementary programming techniques for Bioinformatics, including script programming, some UNIX basics, and relational databases. Please contact Lars Arvestad. For additional information. The course is offered by CSC. And is held in English in period 2 (Nov/Dec). Omic Data and Systems Biology, DD2399, 7.5 ECTS. Please contact Jens Lagergren. For additional information. The course is offered by CSC.
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MetaTM Home
http://metatm.sbc.su.se/index.html
MetaTM is a consensus method for predicting transmembrane (TM) topologies. It is based on support vector machine models and combines the results of six TM topology predictors and two signal peptide predictors. MetaTM is available as a DAS server. Use DASher. To query protein IDs and display MetaTM's results. MetaTM has been published in BMC Bioinformatics. Read it here. The MetaTM homepage is on-line. 2008 · Klammer, Messina and Sonnhammer ·.
Documentation
http://www.orthoxml.org/xml/Documentation.html
OrthoXML version 0.3. SeqXML version 0.4. Have questions or suggestions? OrthoXML example v0.3. SeqXML example v0.4.
Phobius
http://phobius.cbr.su.se/index.html
A combined transmembrane topology and signal peptide predictor. Paste your protein sequence here in Fasta format:. Select the sequence file you wish to use.
Reference proteomes
http://www.orthoxml.org/xml/Reference_proteomes.html
SeqXML versions of the reference proteomes. Release 5 (2011 04). All 66 species in one tarball. FASTA versions available at. The Reference Proteomes group provides complete non-redundant proteome sets for species chosen by the Quest for Orthologs. Group 66 species are publicly available and are generated using UniProt and/or Ensembl. More information is available from our partners at the EBI. And at the Reference Genome Annotation Project. Have questions or suggestions?
Introductory courses for PhD students in chemistry - Kemiska sektionen
http://www.kemi.su.se/forskning/utbildning-på-forskarnivå/outline-introductory-courses-for-phd-students-in-chemistry-1.144249
Gå vidare till:. Kris- och stödinformation för studenter. Introductory courses for PhD students in chemistry. Introductory courses for PhD students in chemistry. Apply for each course at the latest seven days before the start of the course. For further information please contact Paula Jokela, paula@kol.su.se. Outline introductory courses for graduate students in chemistry 2016/2017. 1 Teaching chemistry (2 P, code KZ41DKE). 9 to 12, Monday 12 September. 9 to 12, Wednesday 14 September. Tony Burden, MND.
Download the functional coupling/association networks. - FunCoup
http://funcoup.sbc.su.se/downloads
FC30 A.thaliana full.gz. FC30 C.elegans full.gz. FC30 C.familiaris full.gz. FC30 C.intestinalis full.gz. FC30 D.melanogaster full.gz. FC30 D.rerio full.gz. FC30 G.gallus full.gz. FC30 H.sapiens full.gz. FC30 M.musculus full.gz. FC30 R.norvegicus full.gz. FC30 S.cerevisiae full.gz. The full format is a tab-separated value (TSV) format with the following columns:. The final Bayesian score (FBS) of the strongest coupling class. The Ensembl gene identifier of the gene pair. FC30 A.thaliana compact.gz.
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Steps to Get Started:. Click “Add to Cart.”. Confirm your order total and click “Checkout.”. Enter your billing information and click “Purchase.”. San Bernardino Food Handler Course. Partners with San Bernardino County Department of Public Health. Upon successful completion of the course and test, you will print your San Bernardino County Department of Public Health Food Handler Certification Card, which will be valid throughout San Bernardino County. Fully Audio/Visual Learning Experience. Provides an u...
Stockholm Bioinformatics Center
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