Hi Ugur,

you should blast the sequence at the NCBI against the T. monococcum Genome to get the answers to your questions.

regards

Stephan

Hi Stephan,

Thank you for feedback firstly. As far as I know, there is no available T. monococcum genome sequence in NCBI. Or maybe I couldn't find mentioned link. So, İf you can send me the more clear detail about it, I would be so appreciate to you. Tkanks in advance.

With my best regards

Uğur

Hi Ugur,

I already found in the NR Database some Sequences, you also may look in all other databases like WGS, GGS and so on.

Just have a look at the attached file.

The HP is here:

https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch

Also just type here T. Monoccocum, that will show you all sources:

https://www.ncbi.nlm.nih.gov/

If you have any questions just let me know.

kind regards

Stephan

Hi Stephan,

Thanks again for valuable informations.I got search by using the sequences for triticum monococcum and triticum aestivum etc. also. but I couldnt get any result. I wonder if I did not use the tools or there is no genomic data under triticum species? Im sharing the proccess photos as attached. Could you glance it.

Thanks

With my best reagrds

Uğur

Hi Ugur,

may be the Sequence you are looking for, is not present within the genome, that is in the "Nucleotide collection" database.

1.

-You should try all the other databases (but with a decreased threshold; see point 2) like

whole genome shotgun contigs (WGS)

Genomic survey sequences (GGS)

refseq

ESTs

TSA

and so on, to see in which databases monococcum sequences are

If none of them work you still could try the SRA (Short read Acrchive), but for this you need the particular SRA-Experiment number, which is a little hard to find at NCBI

2.

- you also could decrease the threshold (further down on the homepage)

especially for such short sequences

switch from " Highly similar sequences (megablast)"

to "More dissimilar sequences (discontiguous megablast)"

or

to "Somewhat similar sequences (blastn)"

3.

If you still have any other sequence database, you could try to blast there, increase the size of you DNA-Sequence with the surrounding sequences and try again to blast it as a larger segment at NCBI.

best wishes

Stephan

Hi Stephan

We got the problem at ensembl.org and we have the sequences. Thank you so much for your sincerely interest.

Best regards