User: SRKR

gravatar for SRKR
SRKR170
Reputation:
170
Status:
Trusted
Location:
Visakhapatnam
Website:
http://srkrlab.com/
Twitter:
ravikanthtweets
Scholar ID:
Google Scholar Page
Last seen:
2 years, 4 months ago
Joined:
6 years, 8 months ago
Email:
s***********@gmail.com

I am a Research Scholar pursuing my Ph. D. in Bioinformatics from Andhra University, Visakhapatnam, Andhra Pradesh, India. My areas of interest include tool designing and database development.

Posts by SRKR

<prev • 27 results • page 1 of 3 • next >
0
votes
1
answer
917
views
1
answers
Comment: C: Extraction of Intergenic Regions and Features from Gene Coordinates and Gene Det
... Yes considering it as a circular genome. Sorry didn't mention that in question. ...
written 2.3 years ago by SRKR170
0
votes
1
answer
917
views
1
answer
Extraction of Intergenic Regions and Features from Gene Coordinates and Gene Details
... I am looking for a code logic to extract intergenic sequences based on the coordinates of the genes, and also to assign distal and proximal gene names and strats. But am stuck with overlapping complications. Could you please share code logic to address the case given below. **Gene Coordinates and G ...
logic genes intergenic sequences php written 2.3 years ago by SRKR170 • updated 2.3 years ago by Jeffin Rockey1.1k
0
votes
1
answer
5.2k
views
1
answers
Comment: C: Intergenic Region
... Fabian, I am also looking for a code logic to extract intergenic sequences based on the coordinates of the genes. But am stuck with overlapping complications. Could you please share code logic to address the case given below. **Gene Coordinates and Gene Details - Name and Strand** Start - Stop G ...
written 2.3 years ago by SRKR170
0
votes
1
answer
3.5k
views
1
answer
What Is The Minimum Coverage And Identity Percentage For Protein Domains?
... I am trying to find out existence of protein domains in a set of sequences. I am using BLASTX for the task. I have made a BLASTX of my sequences with the ProDom sequences. I used an e-value cutoff of 1e-3. What should be the identity percentage and the coverage percentage of the domain so that I can ...
written 5.4 years ago by SRKR170 • updated 5.4 years ago by Manu Prestat3.9k
1
vote
2
answers
2.8k
views
2
answers
Answer: A: Split Fastq Files With A Pattern
... You can use simple regular expression to get it done. This is the regular expression you need to search for (@[^\n]{1,}\n)([ATGC]{1,})CCGCGATAT[ATGC]{4}TCCAAC([ATGC]{1,})([\s]{1,}\+[\s]{1,}[^\n]{1,}\n) Then simply replace it with \1\2\4\1\3\4 This will remove your linker sequence completely an ...
written 5.4 years ago by SRKR170
0
votes
0
answers
1.4k
views
0
answers
Comment: C: Logic To Get Consensus Sequence
... I can use IUPAC codes, but those are just being ignored by the application thus affecting the alignment. I am using MEGA 4.0. Also even if the application takes random base based on the letter, that would be technically a glitch. ...
written 5.4 years ago by SRKR170
2
votes
0
answers
1.4k
views
0
answers
Logic To Get Consensus Sequence
... I have a set of aligned sequences in fasta format. I want to get consensus out of the alignment. In case of most of the sites one of the base is showing maximum occurrence. In case of sites where two or more bases occur equal number of times, which base should be taken. An example is given below: ...
consensus bioinformatics genomics written 5.4 years ago by SRKR170
2
votes
0
answers
880
views
0
answers
How To Screen Genomes For Compositional Studies?
... I am working with around 2600+ genomes and wish to study the genome, gene and intergenic features among various groups. In case of taxonomical groups which have very few representatives, there is no issue. In case of taxonomical groups having multiple genomes, on what basis shall I remove similar ge ...
bioinformatics genomics written 5.5 years ago by SRKR170
1
vote
2
answers
2.4k
views
2
answers
Answer: A: How To Map Peptides To Genomic Locations (Hg19)
... Simply do a blastx of your genome with the peptide sequences. Convert the peptide sequences into multifasta format (you can use excel and microsoft word for this). Install command line blast. 3.Convert the peptide sequences into a blast database using the makeblastdb tool. Do a blastx of the genom ...
written 5.6 years ago by SRKR170
0
votes
0
answers
1.2k
views
0
answers
Should Regulatory Regions Be Included In The Intergenic Sequences?
... I am working on finding the functional signatures/remains of regulatory regions, RNAs and proteins in the intergenic sequences (IGs) of E. coli K12 MG1655. I have a few doubts regarding the demarcation of IGs and inclusion of regulatory regions (esp, promoters) in the IGs. Please clarify me the rega ...
genome annotation promoter written 5.6 years ago by SRKR170 • updated 5.2 years ago by Biostar ♦♦ 20

Latest awards to SRKR

Popular Question 4.5 years ago, created a question with more than 1,000 views. For What Is The Minimum Coverage And Identity Percentage For Protein Domains?
Teacher 5.2 years ago, created an answer with at least 3 up-votes. For A: How To Use Blast To Find Exact Matches Of Short Sequences?
Autobiographer 5.2 years ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1031 users visited in the last hour