Searching Repeats And Palindromic Sequences In Dna Sequences
4
4
Entering edit mode
11.9 years ago
Pappu ★ 2.1k

I have many DNA sequences with ~500-1250 bp each. I want to find out possible repeats and palindromics sequences upto length 12 in these sequences. I have tried several web servers without any avail. Here is an example of DNA sequence:

TGTCAGCTACCTTGATGGATTGAGTTTGTTTCGGTCGATGCTCCATCGGGAGAGAGTCTG
CGTCCTGGTCCGAGCAAGTCCCACCAAGTGGCACTTGGCGGCGCCATGTCCTATCTAGTG
CCACCATGTCCGAGGACTTTGATGGCACATGGTGGCACTTGATTTGCCCAAGTCCCACCT
GCTCCGACGTGGACCGACTTCGTGGCACATCGCTATCACCCACTCTACCGTTGAAAAGCC
GAAGTCAAGCGCCGAAAGCTGATCGATTTGCGGTGTGATACGTTGCCAGTGATTCGTTCC
GTGGTTTATGCTTGGCGCACCTACCGCGTCCCCGACGCATCGACTCCGCCGCCATTGCGC
GGCACAAAACGGCCTTCGATCCTTCCGTACGGAGGGGTACTGCAGGGCTCACTGTTCATG
CCGGAAATTGCACCGGCTTTTTTTTCAATCAAATCAAGTGGACCGTGTCGGATAGTGAGG
ACACCGGACACCGCGATACCAAGCCGATTGGCGGTCTGTTTGTGAAAATAGACCGTAGTG
CGGACAATTCCGAAGCCGGACACCGGACAGGTGCTCTGTGGAAATTCCGCGTATGCCCGA
CACCCTTACAGCCGCGTGGCTGGGTGCGGATCACGAAGCCCAAAACACTGCGGCGGGGAT
GATCTGACTTTGGGGTGGGGAGCTGCTTTGCGTGCCGAATGACGGCGAACGCAGGCTTCT
GAGCAAATATCGATCCGGGGGGCGCCACCGGTACCAGAACGGCGCAACAGGTAATCACCC
ATCACGGCAAGGGCCGCAGGCGTGTGGACGCAATCCACGCGAAGGCAGGCTCGCATCCAG
AGATGCACCGGATAGGGTGGCCGCGCAAGCGGTGCGTGAGGCGAGAGCCTTGCATGTTCG
CGAAGCGGACGGTCACGACGCATTGCTTCCATGCTCAGGGCCGATCGGTTTGGCATCGCT
AAAGGACCGGAAGAGTGGTTGTAGGACCGGCAGGGTGGGCCGGCAAGCTGGGGGTGGTAC
CCCGGTGCACCAAGCGGGCAGGGCCAATTCGGGGTTGGCGCCGCCGAGAATTGGGTTGCG
CAGATTTGCGCGGCCGGCGGGATGCGCTTAGCGCGAATAGGAATCCGTC
python • 25k views
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5
Entering edit mode
11.2 years ago
Hamish ★ 3.3k

The European Molecular Biology Open Software Suite (EMBOSS) includes some basic tools for finding tandem repeats and inverted repeats (see B.6.22. Applications in group Nucleic:repeats). There are many on-line services providing the EMBOSS tools, for example:

For more sophisticated repeat finding you will want to look at tools using Repbase for example:

Other nucleotide repeat finding methods found by a couple of web searches:

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4
Entering edit mode
11.9 years ago

Try to see what MUMmer can do for you. Also, this can be done with scan_for_matches.

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0
Entering edit mode
11.2 years ago

Have you tried searching for palindromes on biophp.org?

For repeats, I usually try Tandem Repeats Finder but it doesn't find any in your sequence. SelfBlast might be a good option if you are also looking for inverted repeats.

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Entering edit mode
11.2 years ago
Anima Mundi ★ 2.9k

Emboss Palindrome allows you to find palindromes with a minimum and a maximum length.

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