Shishir K Gupta

10 Questions 16 Answers 0 Followers

Questions related from Shishir K Gupta

Which proteins of bacteria are often involved in protein-protein interactions with host?

As I know, the effectors and some secretory proteins of pathogenic bacteria are involved in host interactions but I also read some articles where some groups used the whole proteome of bacteria...

15 December 2013 8,308 5 View

What should be the minimum acceptable accuracy of gene-predictor on gene level?

Due to absence of well annotated gene boundaries, I trained a gene predictor in the absence of UTR training parameters. In such condition what can be the minimum acceptable accuracy of...

05 September 2013 6,180 1 View

How can I find the organism B which is phylogenetically close to organism A on the basis of genome similarity?

I have an organism A which is recently sequenced. I want to find the organisms that are phylogenetically closer to organism A. I want to find the closest organism whose genome should already be...

10 May 2013 9,432 1 View

Error in Sam to Bam conversion.

I want to convert Sam file into Bam. I am using command $ samtools view -b -S -o bowtie.glob.bam bowtie.glob.sam, but I am getting the following error: Parse error at line 25645: invalid CIGAR...

27 February 2013 6,068 5 View

How to build combined library for repeatmasker.

I want to perform repeatmasking on ant genome. Ant is also included in the repeat library obtained from Repbase. The library RepeatMaskerLib.embl also contains my species. However, I also...

11 February 2013 3,083 3 View

How to parse FASTQ file?

I am new to next generation sequencing (NGS). I need to format some FASTQ files. For example, I want to replace characters /1 and /2 with -1 and -2 in the files that have data like...

01 February 2013 3,576 15 View

Could somebody suggest a protocol to identify/search the protein isoforms?

I have a list of immune signalling proteins of Camponotus. I want to identify the isoforms of these proteins. Is it possible to get the isoforms by searching the corresponding genes in NCBI? Is...

30 October 2012 350 2 View

Could somebody suggest a protocol to identify/search the protein isoforms?

I have a list of immune signalling proteins of Camponotus. I want to identify the isoforms of these proteins. Is it possible to get the isoforms by searching the corresponding genes in NCBI? Is...

28 October 2012 6,263 1 View

Sequence selection

Among the multiple entries of sequences for same protein of a specific organism in any database, which entry should be used for further task? Is there is any specific criteria to select such...

06 September 2012 5,805 3 View

What is the difference between canonical and non-canonical signalling pathway?

Could anyone please tell me the difference between canonical and non-canonical signalling pathway.

01 August 2012 401 12 View