*List of molecular graphics systems

Wade, S (2016). "ProSAT+: visualizing sequence annotations on 3D structure". Protein Eng Des Sel. 29: 281-4. doi:10.1093/ ... "PDB list of molecular graphics tools". "Index of Molecular Visualization Resources". "Molecular Visualization Resources by Eric ... Molecular dynamics MM - Molecular modelling, molecular orbital visualizing MRI - Magnetic resonance imaging NA - Nucleic acids ... Visual Molecular Dynamics license Humphrey, W; Dalke, A; Schulten, K (1996). "VMD: visual molecular dynamics". Journal of ...

*Alignment-free sequence analysis

... genome annotation, comparative genomics, molecular phylogeny and gene prediction. The pioneering approaches for sequence ... In bioinformatics, alignment-free sequence analysis approaches to molecular sequence and structure data provide alternatives ... possible number of k-mers for nucleotide sequence: 4k, while that for protein sequence: 20k) in sequences. Each k-mer count in ... Molecular sequence and structure data of DNA, RNA, and proteins, gene expression profiles or microarray data, metabolic pathway ...

*Gene ontology

Cozzetto, Domenico; Jones, David T. (2017). "Computational Methods for Annotation Transfers from Sequence". In Dessimoz, C; ... Methods in Molecular Biology. 1446. Springer (New York). pp. 85-93. doi:10.1007/978-1-4939-3743-1_7. ISSN 1064-3745. Diehl AD, ... Annotations from automated processes (for example, remapping annotations created using another annotation vocabulary) are given ... Full annotation data sets can be downloaded from the GO website. To support the development of annotation, the GO Consortium ...

*E-Science

Proteome Annotation Pipeline, High-Throughput Structural Biology, Global Biodiversity MRC: Biology of Ageing, Sequence and ... Molecular Dynamics, Materials Science and Engineering, Computer Science and Engineering, and Nanotechnology. Structural Biology ... Molecular Environmental Grid, NERC DataGrid The funded UK e-Science programme was reviewed on its completion in 2009 by an ... Structure Data, Molecular Genetics, Cancer Management, Clinical e-Science Framework, Neuroinformatics Modeling Tools NERC: ...

*Genome project

... molecular biology and bioinformatics have created the need for DNA annotation. DNA annotation or genome annotation is the ... Improvements in DNA sequencing technology has meant that the cost of sequencing a new genome sequence has steadily fallen (in ... Rather than sequence a chromosome in one go, it would be sequenced piece by piece (with the prior knowledge of approximately ... The genome sequence of an organism includes the collective DNA sequences of each chromosome in the organism. For a bacterium ...

*STK40

2006). "The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091): 315-21. doi:10.1038/nature04727 ... Molecular and Cellular Biology portal. ... sequencing and analysis of 500 novel complete protein coding ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ...

*CELA3B

2006). "The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091): 315-21. doi:10.1038/nature04727 ... Dec 1988). "Molecular cloning of complementary DNA encoding one of the human pancreatic protease E isozymes". J Biochem. 104 (2 ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ...

*GeneCards

Simplified Molecular Input Line Entry Specification). PharmGKB gives drug/compound and its annotation. Transcripts: This ... Since the 1980s, sequence information has become increasingly abundant, many laboratories realized this and started to store ... Annotation unification: Different data source often offer annotations with heterogeneous naming system. Annotation unification ... unique wealth of combinatorial annotations of human genes. Annotation combinatory: Using GeneDecks, one can get a set of ...

*Geworkbench

Visualization of gene expression (heatmaps, volcano plot), molecular interaction networks (through Cytoscape), protein sequence ... and protein structure data (e.g., MarkUs). Integration of gene and pathway annotation information from curated sources as well ... sets and sequences. Dataset history tracking - complete record of data sets used and input settings. Integration with 3rd party ... sequence, and structure data. geWorkbench is the Bioinformatics platform of MAGNet, the National Center for the Multi-scale ...

*28S ribosomal RNA

The comparison of the sequences from these genes are sometimes used in molecular analysis to construct phylogenetic trees, for ... Several databases provide alignments and annotations of LSU rRNA sequences for comparative purposes: RDP, the Ribosomal ... "Molecular phylogeny of Arthrotardigrada (Tardigrada)". Molecular Phylogenetics and Evolution. 54 (3): 1006-1015. doi:10.1016/j. ... Eperon, I. C.; Anderson, S.; Nierlich, D. P. (1980-07-31). "Distinctive sequence of human mitochondrial ribosomal RNA genes". ...

*Victor V. Solovyev

Genome Biol Solovyev V, Salamov A. (2011) Automatic Annotation of Microbial Genomes and Metagenomic Sequences. In Metagenomics ... easy-to-use desktop application for sequence analysis and molecular biology data management. Besides bioinformatics his ... He is interested in genome structural and functional annotation and applying it for rational design of biological systems. ... Solovyev V.V. (1993) Fractal graphical representation and analysis of DNA and Protein sequences. BioSystems, 30, 137-160. Moroz ...

*DNA

These sequences are usually just molecular fossils, although they can occasionally serve as raw genetic material for the ... May 2006). "The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091): 315-21. Bibcode:2006Natur. ... The sequence on the opposite strand is called the "antisense" sequence. Both sense and antisense sequences can exist on ... The DNA sequence may be aligned with other DNA sequences to identify homologous sequences and locate the specific mutations ...

*UCSF Chimera

... protein sequences with feature annotations), others interfaces to PDB2PQR charge/radius assignment, APBS electrostatics ... of molecular graphics systems Molecular modelling Molecular graphics Molecular dynamics Molecule editor Software for molecular ... others many sequence alignment formats read, written sequence alignments can be created, edited sequences automatically ... multicolor backgrounds standard molecular representations (sticks, spheres, ribbons, molecular surfaces) pipes-and-planks for ...

*De novo transcriptome assembly

Following annotation, KEGG (Kyoto Encyclopedia of Genes and Genomes) enables visualization of metabolic pathways and molecular ... Blast2GO (B2G) enables Gene Ontology based data mining to annotate sequence data for which no GO annotation is available yet. ... Functional annotation of the assembled transcripts allows for insight into the particular molecular functions, cellular ... Whereas high sequence coverage for a genome may indicate the presence of repetitive sequences (and thus be masked), for a ...

*PRINTS

In molecular biology, the PRINTS database is a collection of so-called "fingerprints": it provides both a detailed annotation ... The motifs themselves are not necessarily contiguous in sequence, but may come together in 3D space to define molecular binding ... A fingerprint is a group of conserved motifs taken from a multiple sequence alignment - together, the motifs form a ... The particular diagnostic strength of fingerprints lies in their ability to distinguish sequence differences at the clan, ...

*DPM3

2006). "The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091): 315-21. doi:10.1038/nature04727 ... Molecular and Cellular Biology portal. ... of more than 15,000 full-length human and mouse cDNA sequences ...

*SUHW4

"Prediction of the coding sequences of unidentified human genes. XVIII. The complete sequences of 100 new cDNA clones from brain ... Klug A (October 1999). "Zinc finger peptides for the regulation of gene expression". Journal of Molecular Biology. 293 (2): 215 ... "SNP linked to Gene ZNF280D(geneID:54816) Via Contig Annotation". NCBI. Retrieved 10 May 2014. "Genomatix". Genomatix. Retrieved ... Blom N, Gammeltoft S, Brunak S (December 1999). "Sequence and structure-based prediction of eukaryotic protein phosphorylation ...

*Cn3D

It "simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features ... List of molecular graphics systems Molecular graphics List of software for molecular mechanics modeling Wang Y, Geer LY, ... Chappey C, Kans JA, Bryant SH (June 2000). "Cn3D: sequence and structure views for Entrez". Trends Biochem. Sci. 25 (6): 300-2 ...

*Annotation

... molecular biology and bioinformatics have created the need for DNA annotation. DNA annotation or genome annotation is the ... An annotation (irrespective of the context) is a note added by way of explanation or commentary. Once a genome is sequenced, it ... An annotation is a metadatum (e.g. a post, explanation, markup) attached to location or other data. Often, annotations make ... Marginalia Nota Bene PDF annotation Subject indexing Text annotation Web annotation XPS annotation http://www.merriam-webster. ...

*Mir-181 microRNA precursor

Strozzi F, Mazza R, Malinverni R, Williams JL (February 2009). "Annotation of 390 bovine miRNA genes by sequence similarity ... In molecular biology miR-181 microRNA precursor is a small non-coding RNA molecule. MicroRNAs (miRNAs) are transcribed as ~70 ... International Chicken Genome Sequencing Consortium (December 2004). "Sequence and comparative analysis of the chicken genome ... "Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of ...

*Alfonso Valencia

"Sequence-based feature prediction and annotation of proteins". Genome Biology. 10 (2): 206. doi:10.1186/gb-2009-10-2-206. PMC ... The research focus of this group is mainly on the understanding of how cancer progresses, using a combination of molecular and ... He received his PhD in molecular biology in 1988 from the Autonomous University of Madrid. From 1989 to 1994 he was a ... 2011). "Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia". ...

*Amos Bairoch

While working on PC/Gene he started to develop an annotated protein sequence database which became Swiss-Prot and was first ... From 1988 onward it has been a collaborative project with the Data Library group of the European Molecular Biology Laboratory ... His most important contribution is the input of human knowledge by careful manual annotation in protein-related data. ... A little while later he created ENZYME, a nomenclature database on enzymes as well as SeqAnalRef, a sequence analysis ...

*SLC19A2

2006). "The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091): 315-21. doi:10.1038/nature04727 ... 2010). "Systematic molecular genetic analysis of congenital sideroblastic anemia: evidence for genetic heterogeneity and ... 2005). "Direct genomic PCR sequencing of the high affinity thiamine transporter (SLC19A2) gene identifies three genetic ... cellular and molecular mechanisms". Am. J. Physiol. Renal Physiol. 291 (4): F796-805. doi:10.1152/ajprenal.00078.2006. PMID ...

*ZCCHC17

2006). "The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091): 315-21. doi:10.1038/nature04727 ... Chang WL, Lee DC, Leu S, Huang YM, Lu MC, Ouyang P (Aug 2003). "Molecular characterization of a novel nucleolar protein, pNO40 ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ...

*C3orf70

Molecular Psychiatry. 17: 36-48. doi:10.1038/mp.2010.109. PMC 3252611 . PMID 21042317. Mandrile G, Dubois A, Hoffman JD, Uliana ... Non-identity calculated based on (1-NCBI sequence identity). Figure 5: Divergence rate of C3orf70 with respect to Cytochrome C ... "a protein domain database for functional characterization and annotation". Nucleic Acids Res. Retrieved 2015-04-19. "dbSNP". ... The precursor protein has been predicted with a molecular weight of 27.8kdal and an isoelectric point of 4.67. With 33 serines ...

*VectorBase

2007). "Genome sequence of Aedes aegypti, a major arbovirus vector". Science. 316 (5832): 1718-23. Bibcode:2007Sci...316.1718N ... 2008). "Anatomical ontologies of mosquitoes and ticks, and their web browsers in VectorBase". Insect molecular biology. 17 (1 ... mainly genome annotation). Aedes aegypti Anopheles gambiae Culex quinquefasciatus Ixodes scapularis Pediculus humanus Rhodnius ... 2002). "The genome sequence of the malaria mosquito Anopheles gambiae". Science. 298 (5591): 129-49. Bibcode:2002Sci...298.. ...