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Questions related from Muhammad Sufian
Whatever field of research we are in, we usually employ many commercial softwares for the analysis of our results. Whether it is Biology, Chemistry or Physics; we cite the commercial software with...
01 January 2016 5,454 5 View
I want to find out the overall protein sequence similarity among 2 strains of same bacterial specie. Let say, strain 1 has 4500 proteins and strain 2 has 4300. My strategy was; I performed...
11 November 2015 8,774 4 View
I have downloaded complete protein sequences of some bacterial genomes in March 2014 from following NCBI FTP site, ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/ I had a list of NCBI GIs which were...
03 March 2015 4,302 4 View
I have 100 clusters of paralogous protein sequences, each cluster containing at least 50 sequences having 80% sequence identity among them (determined using CD-HIT). To visualize the MSA of these...
05 May 2014 3,889 1 View
I have a list of thousands of NCBI-GIs of proteins. I want to determine; 1. how many of them are enzymes ? 2. what are their EC numbers ? 3. What is the reference database for this information...
03 March 2014 6,632 3 View
############################################# UPDATED Now consider following two proteins; http://www.ncbi.nlm.nih.gov/protein/194443845 http://www.ncbi.nlm.nih.gov/protein/194443076 In previous...
02 February 2014 3,627 7 View
I have got a long list of gene acronyms e.g., proS pheS glyQ and so on....... I want to convert them to full names e.g., proS = prolyl-tRNA synthetase pheS = phenylalanyl-tRNA synthetase glyQ =...
02 February 2014 5,938 4 View
There is a protein in Salmonella enterica serovar Typhi with the title "Unidentified ORF" (YP_005216057.1, GI:378958571). What does it mean ? Since as per my thinking, ORF is concerned for nucleic...
01 January 2014 8,798 5 View
I have a single text file containing amino acid sequence of ~6000 proteins in FASTA format. All proteins belong to a single species, but different strains. I want to determine COG...
01 January 2014 8,677 10 View
Using Geneplotter R package, there is a function named plotMA (http://www.bioconductor.org/packages/2.13/bioc/manuals/geneplotter/man/geneplotter.pdf). To get the plot, your object (data.frame)...
01 January 2014 5,659 1 View
I have ~17k amino acid sequences in FASTA format in a single file. Using following command of Clustal Omega on Linux system, I created the distance matrix; clustalo -i filename.faa...
01 January 2014 2,071 4 View
I have 42 FASTA files, each containing ~400 amino acid sequences. I want to sort out those sequences which are identical in all 42 files, e.g. sequence of Protein A is identical in all 42 files.....
12 December 2013 9,073 17 View
There are 43 reported serovars of Salmonella enterica reported on NCBI Genome. There are few articles describing selective comparison among few serovars (one attached). I want to know the...
12 December 2013 952 1 View
I have a KEGG database Brite hierarchy file, in which the data is present in following form; test-file C 0001 Carbon [C] D SAR001 methane [CH3] D SAR002 ethane D SAR003 propane D SAR004...
12 December 2013 8,510 29 View
I have a query that whether there is any restriction enzyme (endo or exo) which can cleave both ssDNA or dsDNA?
04 April 2013 2,337 6 View
PCR and Southern blotting differ per methodology and the majority of us here know these techniques in detail. But I was wondering why a researcher would prefer to conduct a Southern Blot over PCR,...
01 January 2013 4,235 16 View
