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A database of maize genomic sequences, searchable by BLAST, by repeat sequences, and sequence name, gene name, locus, or other landmark. TIGR is a member of the Consortium for Maize Genomics. The Consortium received a funding award from the National Science Foundation in September 2002, to evaluate two gene-enrichment techniques, methylation filtration and high Cot selection, to sequence the maize 'genespace'. Draft assemblies of 287 maize BAC clones selected by the maize community and the Consortium were also produced in the Consortium project. We have recently developed an improved version of the TIGR annotation pipeline optimized for maize genomic assemblies. The latest maize genomic assemblies obtained by gene-enrichment (AZM5) and the 287 maize draft BAC assemblies have been annotated using the improved pipeline. Gene model annotation and functional annotation can be accessed via the TIGR maize BLAST server or the TIGR maize gbrowse display. The first version of the Maize Repeat Database contained 485 characterized maize repeat sequences from the TIGR Cereal Repeat Database. To these we added repetitive sequences downloaded from GenBank and a file of retrotransposon sequences compiled by Phillip SanMiguel (Purdue University). In addition we searched our maize genomic assemblies (AZMs) to identify new repeats. Any sequence within an AZM that showed at least 80% identity over a minimum stretch of 100 bp with an entry in the TIGR Cereal Repeat Database was coded accordingly and added to the Maize Repeat Database.

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• SciCrunch
• 17 years ago - by Anonymous

A Web-based tool that allows users to input a set of exonic variants to score them for a number of features (such as changes in splicing regulatory elements) that have been shown to be predictive of known genome variations that cause exon skipping or activation of ectopic splice sites. In this way, variants can be either prioritized for further splicing-based functional analysis or the results can be used as further genomic evidence in cases in which the causative variant is already known.

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• SciCrunch
• 13 years ago - by Anonymous

A blog about functional MRI from a lab at UC Berkeley.

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• SciCrunch
• 15 years ago - by Anonymous

A quality control software package specially for bisulfite sequencing experiments. It can comprehensively evaluate the quality of BS-seq experiments and automatically trim nucleotides with potential technical biases. In addition, BSeQC also support removing duplicate reads and keeping one copy of the overlapping segment in paired-end sequencing.

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• SciCrunch
• 13 years ago - by Anonymous

A blog by a neuroscientist (United Kingdom) that takes a skeptical look at his own field, and beyond.

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• SciCrunch
• 15 years ago - by Anonymous

The American Society for Investigative Pathology (ASIP) is a society of biomedical scientists who investigate mechanisms of disease. Investigative pathology is an integrative discipline that links the presentation of disease in the whole organism to its fundamental cellular and molecular mechanisms. It uses a variety of structural, functional, and genetic techniques and ultimately applies research findings to the diagnosis and treatment of diseases. ASIP advocates for the practice of investigative pathology and fosters the professional career development and education of its members. The mission of the Society is to promote the discovery, advancement, and dissemination of basic and translational knowledge in experimental pathology and related disciplines. This shall be achieved by fostering investigation into the pathogenesis, classification, diagnosis, and manifestations of disease through meetings, publications, and educational activities. ASIP welcomes basic and clinical biomedical research scientists as active members.

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• SciCrunch
• 15 years ago - by Anonymous

A software tool for spliced and unspliced alignments and SNP detection of short sequence reads.

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• SciCrunch
• 13 years ago - by Anonymous

Public university based in the city of Liverpool, England. Founded as a college in 1881, it gained its Royal Charter in 1903 with the ability to award degrees and is also known to be one of the six original 'red brick' civic universities.

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• SciCrunch
• 14 years ago - submitted by Eddy Kim

Database of transcription factor sequences from a single plant species (over 2,500 genes). It is possible to search: # 1,159,022 gene-space sequence reads (GSRs) obtained by methylation filtering from the Tobacco Genome Initiative (TGI). # The DFCI Tobacco Gene Index (Release 4.0 July 5, 2008) that contains 163,524 tobacco EST sequences and 2,288 expressed transcripts (ETs). # The complete TOBFAC database of tobacco transcription factors. It is also possible to search multiple libraries in a single search. They have incorporated tools for downloading all of the sequences from the blast results and also a contig tool to assemble any or all of the resulting sequences. They are also improving the TOBFAC sequences by extending the original contigs using a contig extension tool designed by Ryan Thompson. This has allowed them to refine the predicted genes. These will be updated on a gene family basis as the improved data become available.

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• SciCrunch
• 13 years ago - by Anonymous

The International Agency for Research on Cancer (IARC) is part of the World Health Organization. IARC''s mission is to coordinate and conduct research on the causes of human cancer, the mechanisms of carcinogenesis, and to develop scientific strategies for cancer prevention and control. The Agency is involved in both epidemiological and laboratory research and disseminates scientific information through publications, meetings, courses, and fellowships.

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• SciCrunch
• 15 years ago - by Anonymous

Software package to calculate sequence quality statistics and create visual representations of data quality for Illumina's second-generation sequencing technology.

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• SciCrunch
• 13 years ago - by Anonymous

From time to time the Editor of Health and Stress interviews leaders in the field of stress management on a variety of topics for inclusion in our publications. Some interviews are listed below. For a complete list of interviews and content, you must be a member of AIS and access the Archives.

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• SciCrunch
• 15 years ago - by Anonymous

The mission of AIS is to improve the health of the community by setting the standard of stress management in education, research, clinical care and the workplace. The American Institute of Stress educates medical practitioners, scientists, health care professionals and the public; conducts research; and provides information, training and techniques to prevent human illness related to stress.

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• SciCrunch
• 15 years ago - by Anonymous

BrainImmune is a free web-based reference that provides comprehensive and up-to-date information on the broad spectrum of medical research related to brain-immune interactions and their impact on health and disease. BrainImmune is written collaboratively by experts in the field from all around the world. Here, concise summaries of basic and clinical research describe how the brain and the immune system ''talk'' to each other in order to maintain homeostasis. BrainImmune is continually updated, with articles and opinions on history, the present state of the art, and new ideas and conceptual frameworks for the neurohormonal- and stress-immune interactions and their implications for common human diseases. Our goal in developing BrainImmune is to facilitate and advance neuroendocrine-immunology research, and the communication and collaborations in this vast interdisciplinary area.

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• SciCrunch
• 15 years ago - by Anonymous

A web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways.

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• SciCrunch
• 13 years ago - by Anonymous

International Neuroinformatics Coordinating Facility (INCF) Funding is an overview of funding opportunities for neuroinformatics research and infrastructure. This list is not comprehensive and we are continually adding to it.

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• SciCrunch
• 15 years ago - by Anonymous

Public research university in Lisbon, and the largest university in Portugal. It was founded in 2013, from the merger of two previous public universities located in Lisbon, the former University of Lisbon and the Technical University of Lisbon.

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• SciCrunch
• 16 years ago - submitted by Andrea Stagg

The NIF Standard Ontology (NIFSTD) is a collection of modular ontologies that provides an extensive set of terms and concepts important for the domains of neuroscience and biology, as well as the data and resources relevant for the life sciences. It is a core component of the Neuroscience Information Framework (NIF) project, a semantically enhanced portal for accessing and integrating neuroscience data, tools and information.

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• SciCrunch
• 15 years ago - by Anonymous

A database of transcription factors from 13 plant species, and PCR primers for around 90% of them.

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• SciCrunch
• 13 years ago - by Anonymous

Arabidopsis thaliana promoter binding element database that focuses on specific binding elements on known genes, found with experimental methods.

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• SciCrunch
• 13 years ago - by Anonymous