filter repeated region

Question

[marghe08]

I'm using blastn locally. The database that I use is "human_genomic". How can I filter the repeated region of the genome?

[st.ph.n]

Use the masked FASTA version as the db.

[mforde84]

depending on what you have in mind, you might want to filter low complexity regions as well. e.g., dustmasker https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/dustmasker/

[marghe08]

I'm using locally the human genomic database. I would like to have only the human genomic contig sequences with NT _ #### Accessions or CM_#####