Genomic and protein sequence databases and tools
Comparative genomic tools and databases: providing insights into the human genome
... of genomic sequence from multiple organisms has provided biomedical scientists with a large dataset for orthologous-sequence ...cross-species sequence comparisons to identify biologically ...
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Comparative genomic tools and databases: providing insights into the human genome
... of genomic sequence from multiple organisms has provided biomedical scientists with a large dataset for orthologous-sequence compar- ...cross-species sequence comparisons to identify ...
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Genomic tools and selective breeding in molluscs
... breeding. Genomic techniques have the potential to revolutionize hatchery-based selective breeding by improving our understanding of the characteristics of mollusc genetics that can pose a challenge for intensive ...
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Development of Genomic Markers and Mapping Tools for Assembling the Allotetraploid Gossypium hirsutum L. Draft Genome Sequence
... flanking sequence based on the BES reference should theoretically be correct for TM-1 which can represent cultivated cotton with expectedly low levels of overall diversity and high levels of synteny; this ...
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kClust: fast and sensitive clustering of large protein sequence databases
... of protein sequences from genome sequencing and metagenomics projects, methods that can cluster huge sequence sets in a reason- able time are in great ...need. Tools that are sensitive enough to ...
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Genome sequencing and next generation sequence data analysis: A comprehensive compilation of bioinformatics tools and databases
... prerequisite genomic sequences and supporting data to understand genome wide functional regula- tion of gene expression and metabolic pathways re- ...of genomic data presents a significant challenge for ...
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Statistical Data Mining for Symbol Associations in Genomic Databases
... mining tools, the objective of our method is to algorithmically reduce combinatorial explosion in searching for sizeable intersections from collections of ...generic databases to more specific genesets can ...
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Signal processing methods for genomic sequence analysis
... In this chapter, we propose a new approach for representing and aligning RNA pseudoknots. The proposed method is based on profile context-sensitive hidden Markov models (profile-csHMMs) [129], which can in principle ...
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Computational approaches to interpreting genomic sequence variation
... Summary The number of variants identified in the genome has grown dramatically over the past several years, and this rich dataset has both inspired and challenged efforts to use computational techniques to functionally ...
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Biological Databases and Protein Sequence Analysis
... primary databases gave rise to serious and valid questions on the format of the sequences, reliability and the comprehensiveness of the ...software tools which are used for analysis accept the data in ...
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Supervised learning for detection of duplicates in genomic sequence databases
... Results and Discussion Binary classification The binary classifiers have high performance, as shown in Table 5. Most have over 90% accuracy and all substantially outperform the Seq90 sequence similarity base- ...
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Using Genomic Databases for Sequence-Based Biological Discovery
... nucleotide sequence comparisons between all UniGene clusters from each pair of ...a sequence in a common ancestor and most likely share common characteristics such as domain structure and biological ...
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Molecular evolution of herpesviruses: genomic and protein sequence comparisons.
... tional extremes (Table 2); (ii) with respect to distance order- ings within and between herpesvirus genomes (Tables 3 to 5; Fig. 1); (iii) with respect to partial orderings for the vecto[r] ...
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Sequence determinants of protein aggregation: tools to increase protein solubility
... of protein systems in which it has been shown that point mutations may dramatically affect the amount of aggregate formation; these include the P22 tailspike protein, single-chain antibodies, interferon-γ, ...
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Using Relational Databases for Improved Sequence Similarity Searching and Large-Scale Genomic Analyses
... a sequence library, one can tailor various scoring parameters to the evolutionary distance being ...high protein sequence identity (70% to 85%, on ...
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Molecular Databases and Tools
... two protein or nucleotide sequences was to create a dot ...a sequence against itself as internal repeats, tandem genes, repeated domains in proteins and regions of low complexity can be ...
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Computer-Aided Protein Directed Evolution: a Review of Web Servers, Databases and other Computational Tools for Protein Engineering
... computational tools that can provide relevant information for the interpretation of experimental results and have been developed in the last few years in the field of molecular modeling of protein ...
Compressing DNA sequence databases with coil
... DNA sequence databases based on the idea of edit-tree ...compression tools for a large GenBank database file containing Expressed Sequence Tag (EST) ...
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RETRIEVING SEQUENCE INFORMATION. Nucleotide sequence databases. Database search. Sequence alignment and comparison
... Ensemble A nice feature is customizable home page that keeps track of your searches even if done from different computers. Ensemble has many tools for extracting and downloading user- specific aspects of the data ...
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Data Mining of Protein Databases
... For example, each row may describe a protein with specific feature attributes, such as, the proteins molecular weight, its amino acid sequence etc. and a label attribute, such as, whether it is involved in ...
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