related links

UNMC Centers/Departments
The Department of  Genetics, Cell Biology and Anatomy
Center for Clinical and Translational Research & Great Plains Health Research Consortium
Bioinformatics and Molecular Modeling Core Facility
DNA Microarray Core Facility
The Proteomics Core in the Department of Pharmacology and Experimental Neuroscience
The University of Nebraska Next Generation Sequencing (NGS) Core Facility
The University of Nebraska High-Throughput DNA Sequencing and Genotyping Core Facility
The Core Electron Microscopy Research Facility
Mouse Genome Engineering Core Facility
Virtual Microscopy and Imaging Core Facility
Bioinformatics Tools
Tools Type Notes
BLAST Alignment The Basic Local Alignment Search Tool [42] is a similarity search tool. It is used to compare two sequences or search a sequence against a database of sequences. It starts by finding short matches between two sequences and attempts to find the local alignments from the initial matches. Thus, it does not guarantee the optimal alignment, so some sequence hits may be missed.
EMBOSS Software Suite EMBOSS is "The European Molecular Biology Open Software Suite". It is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages
Clustal Omega Alignment ClustalW is a general purpose multiple sequence alignment program for DNA or proteins.
pTARGET Subcellular Localization Prediction pTARGET is a computational method to predict the subcellular localization of only eukaryotic proteins from animal species that include fungi and metazoans. Predictions are carried out based on the occurrence patterns of protein functional domains and the amino acid compositional differences in proteins from different subcellular locations. This method can predict proteins targeted to nine distinct subcellular locations that include cytoplasm, endoplasmic reticulum, extracellular/secreted, Golgi, lysosomes, mitochondria, nucleus, peroxysomes and plasma membrane. Current predictions are based on Pfam database version 19.0.
Bioinformatics Tutorials
DNA Structure - Animated Tutorial
Working with next-generation sequencing data
Bioinformatics Projects
Projects Notes
BioPerl BioPerl is a collection of Perl modules developed for use in biological research.
BioJava BioJava is an open-source project built in Java to facilitate rapid application development in bioinformatics. It provides different routines and parsers for processing biological data.
BioPython BioPython is open source framework developed in python for biological application development.
Ensembl Ensembl is a joint project between EMBL - EBI and the Wellcome Trust Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes.
Galaxy Galaxy is a collection of data analysis tools for biological data sets.
Bioinformatics Resource Sites
Source Notes
NCBI National Center for Biotechnology Information
Bioinformatics.org Bioinformatics Organization.
EMBL-EBI European Molecular Biology Laboratory - European Bioinformatics Institute
BioPortal This website contains a variety of information about bioinformatics resources available at Weizmann Institute and elsewhere.
IUBio Archive This is an archive of biological data and softwares.
Bioinformatics Discussion Groups
Forums Notes
BIOSCI/Bionet It is a set of electronic communication forums for biological scientists.
Bioinformatics.org Bioinformatics Organization.
Bioinformatics Publications
Publications Notes
BioInform Bioinformatics news briefs
Bioinformatics This journal publishes scientific papers and review articles in the field of bioinformatics.
BMC Bioinformatics It is an open access journal publishing original peer-reviewed research article in all aspects of the development, testing and novel application of computational and statistical methods for the modeling and analysis of all kinds of biological data, as well as other areas of computational biology.
Briefings in Bioinformatics An international forum for researchers and educators in the life sciences. The journal publishes reviews for the users of databases and analitical tools of contemporary genetics and molecular biology.

 

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