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
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4 answers
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:
Other nucleotide repeat finding methods found by a couple of web searches:
Try to see what MUMmer can do for you. Also, this can be done with scan_for_matches.
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.
Emboss Palindrome allows you to find palindromes with a minimum and a maximum length.
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