Welcome to Python for biologists Here you'll find resources for learning to program in Python for people with a background in biology Now published: Biological Data Exploration. A complete guide to cleaning, manipulating and visualizing complex biological datasets with Python. If you're looking for the exercise files for any of my books, click here. If you want to get started with writing Python c
PROVEAN (Protein Variation Effect Analyzer) is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein. PROVEAN is useful for filtering sequence variants to identify nonsynonymous or indel variants that are predicted to be functionally important. The performance of PROVEAN is comparable to popular tools such as SIFT or PolyPh
Copy Number Inference From Exome Reads CoNIFER uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes. As exome capture reactions are subject to strong and systematic capture biases between sample batches, we implemented singular value decomposition (SVD) to eliminate these biases in exome data. CoNIFER offers the ability to mix exome sequen
文字列同士がどれだけ似ているかを計算できると便利。 例えば “uri” と “url” の距離は1というふうに計算できるので、名前を間違えた時の候補のサジェストとかに使える。 編集距離とかでググるとみんながんばってRubyで計算してるけど、levenshteinというgemを使ったら簡単だった。 gem install levenshtein require 'rubygems' require 'levenshtein' p Levenshtein.distance("erik", "veenstra") p Levenshtein.distance("shokai", "shokai") p Levenshtein.distance("ahokai", "shokai") p Levenshtein.distance("shokai", "ahokai") p Levenshtein.
SNAP is a program that is part of a gene sequencing pipeline. It takes data from gene sequencing hardware that consists of short chunks of DNA (typically 70-300 base pairs long) called reads and determines where, how well and how unambiguously they match to a given reference genome. This is a computationally challenging problem because reference genomes are big (the human genome is over 3 billio
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