Muhammad Sufian

13 Questions 30 Answers 0 Followers

Questions related from Muhammad Sufian

How to barcode hybrid plants ?

Taxonomic identification of plants can be done by gene barcoding. There are several reported gene markers to be used to barcode unknown species. My question is "Is it possible to identify the...

24 January 2020 6,784 3 View

How can I find out sequence similarity between two proteomes ?

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...

06 November 2015 7,127 3 View

How to present a large dataset of 42x73 records of NCBI-GIs in reader-friendly representation ?

I have some results tabulated in an Excel file, which consists of 42 fields and 73 records, each record comprised of 8 or 9 digit number (PDF attached). I want to represent it in a reader-friendly...

08 June 2015 6,811 3 View

How can I find out enzymes in large dataset of proteins ?

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...

18 March 2014 9,287 2 View

How to convert gene acronyms to full names ?

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 =...

12 February 2014 4,892 4 View

How to determine 'Cluster of Orthologous Groups' for our proteins?

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...

18 January 2014 8,945 9 View

Can anybody help me with Geneplotter R package?

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)...

17 January 2014 3,940 1 View

Manipulating DIstance Matrix file created from Clustal Omega (standalone)

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...

07 January 2014 8,547 3 View

How to sort out common (identical) sequences among 40+ FASTA files?

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.....

22 December 2013 8,782 16 View

What is the difference among Salmonella enterica serovars at proteome level?

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 9,309 1 View

Are there any restriction enzymes which can cut both single and double stranded DNA ?

I have a query that whether there is any restriction enzyme (endo or exo) which can cleave both ssDNA or dsDNA?

08 April 2013 8,623 5 View

Color changes of antibiotic stocks of Ceftriaxone and Ceftazidime from transparent to yellow and orange. Does anyone know the reason for this?

I have made the stocks of both antibiotics of conc. 100 ug/ml, dispensed aliquots in fresh eppendorfs by syringe and stored them at -20C. Gradually their color starts changing from transparent to...

07 April 2012 9,860 28 View

Need E.coli F-ve strain sensitive to Ampicillin, Chloramphenicol, Sulfamethoxazole, Streptomycin and Nalidixic acid

I need a recipient E. coli strrain (F negative) for conjugation experiment, sensitive to the following 5 antibiotics, and resistant to any other 3rd or 4th generation...

20 November 2011 2,268 5 View