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 thaandavakeli lolaaya ..

sada sivaa .. sanyasi .. thaapasi kailasavasi […]

Bioinformatics for personal genome interpretation

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 […]

Databases and resources for personal genome interpretation





Short variations—SNVs, short indels

1000 Genomes

Human short variants and inferred genotypes


Short variants from all species


Human short variants […]

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 informatics and computing more generally have alsoincreased. A colleague from […]

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

IMG Home

python 正则表达 前向界定与后向界定

>>> a ‘[acyl-carrier-protein] S-malonyltransferase [EC:]’ >>> b = re.findall(r'(?<=\[EC:).+?(?=\])’,a) >>> b [‘′] >>> b = re.findall(r'(?<=\[).+?(?=\])’,a) >>> b [‘acyl-carrier-protein’, ‘EC:′]



‘(?<=…)’ 前向界定


‘(?=…)’ 后向界定


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


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 ./s1_1.fastq […]

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 describes the genome and metabolic pathways of a single organism.

BioCyc is a […]

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,


dic_cog_annot[h2[1]]={‘orthologous_group':h[3]} dic_cog_annot[h2[1]]={‘protein_annot':h[4]}



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”