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Search: Posts Made By: dineshkumarsrk
Forum: General 06-13-2019, 05:02 AM
Replies: 0
Views: 2,218
Posted By dineshkumarsrk
How to reverse complement the nuclotides, if the coordinates are in reverse order?

I have the series of coordinates in id.txt file, whose coordinates sequences are in genome.fasta file. The coordinates of id.txt file is shown below,
Contig3:15-7
Contig2:5-10
Contig1:12-3

The...
Forum: Bioinformatics 04-05-2019, 11:50 PM
Replies: 0
Views: 950
Posted By dineshkumarsrk
Question Is it possible to print DNA sequences of subject organism in tblastn?

I did tblastn analysis by following command
tblastn -query t3ss.fasta -subject org1.fasta -outfmt '6 qseqid qstart qend sseqid sstart send pident length evalue sseq' -out org1.xls
It prints the...
Forum: Bioinformatics 03-25-2019, 06:46 AM
Replies: 0
Views: 495
Posted By dineshkumarsrk
Question How to specify output format in stand alone emboss-SKIPREDUNDANT tool?

Hi all, I have been making non-redundant sequence database for BLAST analysis. Therefore, I have used stand alone emboss-skipredundant tool. It works perfectly, but the output sequence fasta headers...
Forum: Bioinformatics 03-23-2019, 03:35 AM
Replies: 0
Views: 623
Posted By dineshkumarsrk
Question How to generate partition file for raxmlHPC analysis?

Hi all, I need to conduct evolutionary analysis by raxmlHPC, wherein I have to to follow the model as given below,



I have phylip alignment file generated by CLUSTALW, which consist 31...
Forum: Bioinformatics 03-16-2019, 01:26 AM
Replies: 0
Views: 673
Posted By dineshkumarsrk
Question How to specify/calculate subject coverage in tBLASTn

I have been screening the homologous gene sequences from my genome of interest by doing tBLASTn, wherein I have to specify two mandatory parameters such as,
Coverage = 40% and Percentage of identity...
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