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The main reason is because the genetic differences between individuals of the same species are tiny. For the vast majority of studies, they can simply be ignored. Differences between individuals are usually (not always, but mostly) differences in SNP genotypes. These are single nucleotide differences which, while they can have phenotypic effect, don't ...


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There are some databases in which you can search for E.coli gene expression data: GenExpDB: E. coli Gene Expression Database Many Microbe Microarrays Database (M3D): A resource of microbial gene expression data Stanford MicroArray Database (use the search tool to find relevant organisms) Colombos (COLlection Of Microarrays for Bacterial OrganismS) ...


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I would suggest searching the name in any trusted genetics database such as NCBI's GenBank (http://www.ncbi.nlm.nih.gov/genbank/). You can just Google search it, but it may take a little longer to find useful information that way. I hope this helps and good luck with your research, CDB


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BAM is the current standard for sequence alignments, and can be used to store unaligned reads/sequences, but when used for unaligned sequences also contains unused alignment data that would bloat the file. An alternative way to compress a DNA sequence file is via 2-bit (or 4-bit encoding) which can compress the sequence content by 75% (in 2-bit encoding, ...


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A 3D model of a (bio)moelcule represents a physical 3-dimensions. For an experimental structure, each atom has a 3D coordinate (x, y, z) and, if determined by crystallography, an additional isotropic or aniosotropic B-factor (that models atom fluctuations). A '1D' SMILES is not a physical 1-dimensional representation, and can be converted to a graph ...


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Was getting long in the comments. In light of your comments, you might be interested in Gene-set enrichment analysis (GSEA). You can do a GSEA using your set, the other one coming from reference databases such as MSigDB (see here). You can categorize your list by gene families using this technique for example. You can get an idea of what cellular process ...


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It depends; what species are the genes from? Some organisms have extensively annotated genomes, and actively curated species-specific databases, while other species may not even have a reference genome sequence available. By itself, a priori, if you were lucky, about all you list would tell you was how to spell the names of those genes--if you're lucky. But ...


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Evolution Evolution is the accumulation of genetic mutations that results in phenotypic variation (physical characteristics) where surviving variations are more suited to the environment the organism lives in, thus allowing it to survive better and -- critically -- reproduce as-good-as or better-than its competing organisms. In terms of computer ...


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Question 1: The phenomena you describe in which it matters whether you have one or two copies of an allele (e.g., the AA phenotype being different than the Aa phenotype) are known as dominance effects. Dominance effects can interact with epistatic effects (in which the phenotypic effect of one locus depends on the genotype at the another locus). One good ...


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A 'good' phylogenetic tree would be completely refined, properly binary, have high bootstrap support for all its branches, and reconstruct clades we think exist with high support values. Generally high support values(there are other methods besides bootstrapping but that is a question for another time) is a measure of a good tree. There are other concerns, ...


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Please note that these are just analogies not exact definitions. Okay so let's imagine DNA as string of 4 letters that is the program code of an organism. Also the running environment is a good analogue to the biological environment (RAM, CPU time, disk space - as resources like food, water etc.) Genes of organism could be imagined as methods of an object ...


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Also try putting the list through Reactome or String DB to see if you see mapping to certain pathways. http://string-db.org/ You can also put lists through ConceptGen to carry out ontology based analyses http://portal.ncibi.org/gateway/conceptgen.html


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BFQ = binary fastq Described here: http://ngsutils.org/modules/fastqutils/ I have not used it myself, but I gather that the maq aligner package can use (or generate) these files. Even though the bam format already incorporates the block compression (described by yourself and others), we routinely deal with gripped bam files and my sense is that there is some ...


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Proteins evolve and have different sequences between species, so you would have to define what you mean with "same protein". One option would be to use an orthology database like eggNOG. (eggNOG has the same protein identifiers as STRING.) Then you could figure out 1:1 correspondences between proteins. You probably also want to read up on Roded Sharan's ...



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