If I have a predicted sequence for a protein and I want to find where it is located on a genome and find other similar sequences to it on the genome, how would I go about doing this and which tools would be best for this task?
•
written
by
Andy •
1 answer
If we are talking about organisms without introns, it is very simple. A tool to use is tblastn which can be accessed from the main BLAST page. You can download the BLAST package and run the search locally. There are many other sequence search programs such as DIAMOND that can perform the same type of analysis.
It is more complicated for organisms with discontinuous genes, but it is the same general principle.
It may or may not, depending on the exact organism. For example, baker's yeast has introns but not many, and most genes in its genome don't have any.
Generally speaking, tblastn is not the best choice for genes that have many short pieces, but you didn't provide enough information for me to give you a definitive advice. You should be able to research this yourself as this is one of the well-understood procedures.
Log in to answer this question.
-
Best way to do protein structure guided similarity search?
written by Mark •
-
How can I find fasta sequences for gp120 and gp41?
written by mark.pekarsky •
-
Any script that can produce different mutations of protein sequences at specified positions?
written by maa4618 •
-
Best way to BLAST orthogroups?
written by MJ Mantas •
-
Genetic Linkage Map and Repetitive sequences
written by Juan Luis •
-
Software/Tool for aligning multiple nucleotide viral genome sequences (n=15; 300kb in length) while…
written by Olivia •
-
How to Extract Full sequences for Low Quality (predicted) Protein Sequences from whole genome data
written by kkumarreddy •
-
Genome annotation: small dataset of genomes
written by gifthorse17 •
-
Annotation with Prokka or RAST.
written by lokraj2003
-
Meaningful clusters in phylogenetic trees
written by n00bgenome •
