Sada siva | Om Namo Shiva Rudhraaya (A special music)

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 thaandava[……]

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Bioinformatics for personal genome interpretation

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[……]

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Databases and resources for personal genome interpretation

 

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[……]

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Editorial: Current progress in Bioinformatics 2012

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 i[……]

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IMG- another microbial genomes database (Get more info than NCBI)

IMG Home

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python 正则表达 前向界定与后向界定

>>> 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[……]

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如何查看显示文件具体某列信息

awk -F ‘\t’  ‘{print $1}’  KO_list_file note:文件以tab分割列表,$1位第二列 […]

Tutorial: Piping with samtools, bwa and bedtools

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 ./s[......]

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Some other replaced databases for KEGG paywalled

  • 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 desc[……]

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python dic problem

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[[……]

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