Dear Arijit

can you used BLAST tool from NCBI

https://blast.ncbi.nlm.nih.gov/Blast.cgi

then click in Nucleotide BLAST and put your sequences

best wish

You could use the loci as input for the VEP (http://www.ensembl.org/Multi/Tools/VEP?db=core)

Hi Yousef, I am trying to get a batch done at once, also the format I have the data in won't work for BLAST. Thanks.

Hi Emily,

VEP also won't help as these are not in any kind of SNP identifier format (I mean not VCF or variant identifier), I just extracted some specific nucleotides along the chromosomes on the basis of some previous analysis and just want to find out which genes those nucleotides belong to (~2000 locations).

Thank you.

Dear Arijit,

As per nature of nucleotide data in your hand, practically it is impossible to find out chromosomal locations or gene locations. specific nucleotide are collected randomly that why sequence similarity searching becomes difficult.

can you know the positions of such randomly selected nucleotides? is it documented in previous analysis?

Life is the game of alphabets (A,T or U,G,C), when you playing with these characters, concentrate on its combinations and permutations.

Dear Mahadev,

Perhaps I haven't made my question clear and I am sorry for that.

What I have is Chromosomal location of a nucleotide in a gene and the location can be easily corresponding to the Dmel genome current release. And also, I could not understand why sequence similarity came into play in your answer, as I do not actually need to align anything. Let me rephrase my question as: "How can I find out which chromosomal location corresponds to which genes"? And by chromosomal location I mean something like the following:

chr2L 197334

chr2L 3468598

chr3R 66457

...

Hope this clarifies the question

Dear Arijit,

The following resources is definitely useful for gene synteny (gene order) analysis.

CoGe: https://genomevolution.org/CoGe/SynFind.pl

Flybase: http://flybase.org/maps/synteny

Try it.

Dear Arijit,

can you not just use the UCSC genome browser and look up your chromosomal positions there?

UCSC genome browser: http://genome-euro.ucsc.edu/cgi-bin/hgGateway

hope this helps

Dear Arijit,

You can retrieve the gene names using BioMart tool in Ensembl Genome Browser (https://www.ensembl.org/biomart/martview/bae7f72cab06b6e41ed44fba972c155e)

I tried the chromosomal locations you mentioned above and it works. Please try the following steps:

1) Select New

2) From "Choose Database" dropdown menu, select Ensembl Genes91 and then from "Choose Dataset" select Fruitfly Genes(BDGP6)

3) In "Filters", go to "Region" and select "Multiple regions (Chr:Start:End:Strand) [Max 500 advised]"

Here, input your locations in the following format:

2L:197334:197334

2L:3468598:3468598

3R:66457:66457

4) In "Attributes", go to "Gene" and select "Gene Name" and other features if you're interested in them.

5) Next to the New button, press "Count" and once it counts those locations in the genome, it will display the number. Then press "Result".

You will have the Gene names. Rest of it is pretty intuitive to export the data in format of your choice (TSV,CSV,Excel etc)

Hope this helps. Good luck!

Utkarsh

PS: Try not to enter all 2000 locations at once. Split it in 4 batches otherwise the page may become unresponsive.

Dear Hannes,

Yes, no doubt UCSC table browser will be suitable tool, but from my experience, they often tend to omit some locations (seems like deliberately) while fetching data. However, I found out a nice server which seems to work perfectly for our needs: https://manticore.niehs.nih.gov/pavis2/

Thank you,

Arijit

This is question is related to finding location, if you know co-ordinates BEDTOOLS works fine and suggested server uses it also