Question: How to extract the mobile genetic elements
0
gravatar for anabio86
5 months ago by
anabio860
anabio860 wrote:

Hi folks, I need to do alinhamento using just the chromosomal DNA, without the mobile genetic elements, I would like to know if there is a bioinformatic tools that can do it from fasta files? thx

sequencing alignment assembly • 333 views
ADD COMMENTlink modified 7 days ago by pltbiotech_tkarthi100 • written 5 months ago by anabio860

I guess you could subset your reference FASTA file to include only the sequences you wish to include. What have you tried?

ADD REPLYlink written 5 months ago by RamRS20k

Are you referring to masking parts of the genome that are repetitive before aligning? repeatmasker is the program used to do this. If you are working with human genome then repeat-masked versions are available.

ADD REPLYlink written 5 months ago by genomax63k

Actually, I am working with bacterial DNA, I need to perform a phylogenetic analysis using references from database, but before to compare with these references I need to remove the sequences that belonged to mobile genetic elements such as plasmids, phages this things

ADD REPLYlink written 5 months ago by anabio860

mobile genetic elements

I think this can lead to some confusion. As a human geneticist I think of transposons when I read mobile genetic elements, and not phages/plasmids/....

ADD REPLYlink written 5 months ago by WouterDeCoster37k

We need lots more information, such as what bacteria, whether it has completed reference genomes etc.

Detecting mobile elements is non-trivial. If your genome is not well curated already the task will be almost impossible. There is also not one single tool which will do all of this. Plasmid finding has its own set of tools (e.g. PlasFlow, PlasmidTron and others), prophages can be detected with PHAST/PHASTER (e.g.). I'm no expert on detection of transposons etc, but there are reviews out there which compare and benchmark many tools (e.g https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-015-0055-3 ).

You will largely have to try things and see what the results look like.

ADD REPLYlink written 5 months ago by jrj.healey11k

I just gave up, seems impossible to do that

ADD REPLYlink written 4 months ago by anabio860

Nothing is impossible. Why Portuguese ('alinhamento')?

ADD REPLYlink written 4 months ago by Kevin Blighe39k

If I understand correctly, you are looking for FASTA files of chromosomes but not plasmids, right? If so, you can download them from NCBI using edirect as follows:

esearch -db assembly -q 'GCF_000008865.2' | elink -db assembly -target nuccore -name assembly_nuccore_refseq | efilter -q 'NOT plasmid[filter]' -source refseq | efetch -format fasta
ADD REPLYlink written 4 months ago by vkkodali980
0
gravatar for pltbiotech_tkarthi
7 days ago by
CIMMYT, Mexico
pltbiotech_tkarthi100 wrote:

If you want to extract novel DNA mobile elements, then you need to findout the presence of Terminal Inverted Repeats and Target Site Duplications. You could predict the TIRs using EMBOSS Einverted Repeat Server and you can manually assess the presence of TSDs, in the case of DNA transposon/MITES (autonomous/non-autonomous). If you want to annotate your sequence based on the identified transposons, you can use censor repeat masking: https://www.girinst.org/censor/. Perhaps this is helpful: https://www.girinst.org/server/publ/AsDRF1/

ADD COMMENTlink modified 6 days ago • written 7 days ago by pltbiotech_tkarthi100
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