Searching Repeats And Palindromic Sequences In Dna Sequences

Question

[Pappu]

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

Answer 1

[Hamish]

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:

• Wageningen Bioinformatics Webportal EMBOSS explorer
• Mobyle@Pasteur
• Soaplab2 Web Services at Vital-IT

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

• CENSOR
  • CENSOR@GIRI
  • CENSOR@EMBL-EBI
• RepeatMasker

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

• Tandem Repeats Finder
• RECON
• RepeatRunner
• REPuter
• Imperfect Microsatellite Extractor (IMEx)
• Spectral Repeat Finder (SRF)
• REPFIND
• CRISPRfinder
• GrailEXP
• CONREPP

Answer 2

[Martin A Hansen]

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

Answer 3

[Leonor Palmeira]

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.

Answer 4

[Anima Mundi]

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