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Sada siva | Om Namo Shiva Rudhraaya om namo siva rudhraya .. om namo sithikantaya .. om namo hara nagabharanaaya .. pranavaaya.. dhama dhama dhamarukanaadanandaaya .. om namo vita lakshaaya .. om namo bhasmangaya .. om namo hima shailavaranaaya .. bramadhaya .. dhimi dhimi thaandavakeli lolaaya .. sada sivaa .. sanyasi .. thaapasi kailasavasi […] http://bib.oxfordjournals.org/content/13/4/495.full Key Points Vast amounts of variation data from genome sequencing studies need to be analyzed to understand its association with various phenotypes. Well-curated databases, reliable tools for gene prioritization and accurate methods for predicting the impact of variants will be essential for the interpretation of personal genomes. Standard and unified protocols […]
Database URL Description Short variations—SNVs, short indels 1000 Genomes http://www.1000genomes.org Human short variants and inferred genotypes dbSNP http://www.ncbi.nlm.nih.gov/projects/SNP Short variants from all species HapMap http://www.hapmap.org Human short variants […] In this issue, we present an annual review of progress in critical areas ofbiomedical computing and informatics. Our ability to collect and storebiological and medical data has continued to increase at astoundingrates over the last few years. As a result, the scientific and technicalchallenges for informatics and computing more generally have alsoincreased. A colleague from […] >>> a ‘[acyl-carrier-protein] S-malonyltransferase [EC:2.3.1.39]’ >>> b = re.findall(r'(?<=\[EC:).+?(?=\])’,a) >>> b [‘2.3.1.39′] >>> b = re.findall(r'(?<=\[).+?(?=\])’,a) >>> b [‘acyl-carrier-protein’, ‘EC:2.3.1.39′] 前向界定与后向界定 有时候需要匹配一个跟在特定内容后面的或者在特定内容前面的字符串，Python提供一个简便的前向界定和后向界定功能，或者叫前导指定和跟从指定功能。它们是： ‘(?<=…)’ 前向界定 括号中’…’代表你希望匹配的字符串的前面应该出现的字符串。 ‘(?=…)’ 后向界定 括号中的’…’代表你希望匹配的字符串后面应该出现的字符串。 例： 你希望找出c语言的注释中的内容，它们是包含在’/*’和’*/’之间，不过你并不希望匹配的结果把’/*’和’*/’也包括进来，那么你可以这样用： >>> s=r’/* comment 1 */ code /* comment 2 */’ >>> re.findall( r’(?<=//*).+?(?=/*/)’ , s ) [‘ comment 1 ‘, ‘ comment 2 ‘] […] awk -F ‘\t’ ‘{print $1}’ KO_list_file note:文件以tab分割列表，$1位第二列 In this tutorial I hope to introduce some of the concepts for using unix piping. Piping is a very useful feature to avoid creation of intermediate use once files. Lets begin with a typical command to do paired end mapping with bwa: #-t 4 is for using 4 threads/cores bwa aln -t 4 ./hg19.fasta ./s1_1.fastq […] PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System have a set of Pathways. Not many prokaryotic genomes are available at PANTHER. List of species here Biocyc BioCyc is a collection of 1962 Pathway/Genome Databases (PGDBs). Each PGDB in the BioCyc collection describes the genome and metabolic pathways of a single organism. BioCyc is a […] dic_cog_annot[h2[1]]={‘orthologous_group':h[3]} dic_cog_annot[h2[1]][‘protein_annot’]=h[4] 以上是增加个protein_annot键值， 如果是以下,将会被替换，只一个键值！ dic_cog_annot[h2[1]]={‘orthologous_group':h[3]} dic_cog_annot[h2[1]]={‘protein_annot':h[4]}
dic[name]=”NA” dic[name] = {‘nr_annot':”NA”} dic[name][‘go_num’]=”NA” dic[name][‘go_info’] = “NA” dic[name][‘kegg_hit’] = “NA” dic[name][‘kegg_annot’]=”NA” dic[name][‘swiss_annot’]=”NA” dic[name][‘cog_hit’] =”NA” dic[name][‘orthologous_group’]=”NA” dic[name][‘protein_annot’]=”NA”
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