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I have to do a search for small DNA sequences in the genome of an organism in ENA. I have the accession number and project id. However, I can't download the whole genome because of the download size and would prefer to do it online if possible. I have a rough idea of the part of the genome I wish to scan in, don't know if that's relevant.

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  • $\begingroup$ Do you want an exact match? Did you try BLAST? You can adjust the parameters according to your needs. $\endgroup$ – WYSIWYG May 4 at 9:53
  • $\begingroup$ Have you already tried to submit accession number into advanced search? ebi.ac.uk/ena/data/warehouse/search $\endgroup$ – Shred May 4 at 11:16
  • $\begingroup$ @WYSIWYG Yes I do need exact matches. BLAST would search it against multiple sequences wouldn't it? I don't see how you can find DNA sequences in a particular genome using it $\endgroup$ – Aman Garg May 4 at 22:49
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While it is much better/easier to download and do the exact search on your own, it is possible to do something similar, online. You can use NCBI-BLAST and increase the word length and mismatch/gap penalty. It also allows restricting the subject space; you can even align two sequences. The BLAST on ENA does not have much flexibility (subject restriction/word length). Perhaps you can look for a duplicate sequence on NCBI.

If this genome is available on UCSC genome browser then you can use BLAT too. However, it only accepts sequences larger than 19nt.

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