jhu99 / mitefinder Goto Github PK

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solomiyah altingia lacademic drmbee 13207437722

mitefinder's Issues

Errorneous MITEFinderII output

I am trying to identify MITE in a published genome sequence using MITEFinder II in Ubuntu14.04 LTS OP system. The following script was used:

./miteFinder -input my/fast/file.fa -output my/mitefinder/out -pattern_scoring ./profile/pattern_scoring.txt -threshold 0.5

The program ran smoothly to produce a fasta seq output of probable MITEs. However, the file consisted of some invalid characters.

Please advise to sort the above problem.

Moreover, it will be good if you can throw some light on (i) explaining the header line of the output fasta sequences; (ii) Possible methods to identify TSD and TIR sequences; (iii) How to classify MITEs based on family; and (iv) tool for design primers from MITE-flanking sequence.

Thanks
Dip

How to keep the actual chromosome name in the output?

Hi,
Thanks for this good tool.
I was wondering, how do you keep the original chromosome name in output fasta header?
miteFInder renames chromosomes to 1,2,3... But it is confusing when we want to do some downstream analysis
do you have any suggestions?
Thanks

for example
`>mite|1|17871177|17871187|17871261|17871271|t4|17871184|m1|ave_score:0.849149
ATTGTTGTTTGGATTGTTGTTTAAGTTTTTTTTTGGAATTATTTTGTGTTTTTGTTAAAA
TTCAAAACGTTTTCCTGTTTTTAAAACGTTTTTTGATTTTTAAAAACGTTTTTCAAGTTT
CCAATAATAAACTATGTATAATAAAACGTTTTTAAAAAATTTTAAAAATATTTAACAACA
TTTTTCTATAATTATAAAAATTTATAATTTTGTAT

mite|1|19986949|19986959|19987279|19987289|t3|19986953|m1|ave_score:0.707483
ACAAAAAAGTGAAACATAAAATATTTCTAAAAGACTAATTTCTTTTTGATGATATTGATA
CTCATGAATATATTTGATATAAATAATAAAGAAGTGTACGAAAAAAACATAAAAAAAAAA`

expected fasta header

mite|Bna.chrA1|17871177|17871187|17871261|17871271|t4|17871184|m1|ave_score:0.849149
mite|Bna.chrA2|17871177|17871187|17871261|17871271|t4|17871184|m1|ave_score:0.849149

Issues in program

Dear Jialu Hu,

Thank you for your great software!
In your paper you mentioned that you clustered the mite candidates into families. However, I did not find the
code for clustering in your program. Could you give me more details about the clustering procedure?

Best regards,
Max

What threshold number should be used if we need the results to be as reliable as possible

Hi dear developer,

Thanks for your great scripts!

I have try some thresholds from default 0.2 to 0.9, and the number of MITEs varied from thousand to several. So I would like to know your suggestion about the threshold to be used if I need the results to be as reliable as possible with the balance bwteen MITEs' count and accuracy?

No header in output

Hello,

I am processing some genomes with mitefinder and here is my commands:
miteFinder_linux_x64 -input genome.fa -output MITE.fa -pattern_scoring ~/Softwares/miteFinder/profile/pattern_scoring.txt -threshold 0.5

In the output of some genomes, there are sequences looks like this:

>mite|17671|2089|2098|2192|2201|t6|2093|m1|ave_score:0.621227
CACACAATAATGTTTAACACACAATAGTGTTTAACACACAATAATGTTTAACACACAATA
GTGTTTAACAAACAATAATGTTTAACACACAATAATGTTTAACACACAATAATGTTTAAC
ACACAATAATGTTTAACACACAATAATGTTTAACACACAATAATGTTTAACACACAATA
CGCGCGAGTAGGTCACCAAGGGGATCTTGTTCCTGCACGACAATG
CCCCGGTTCATAGGGCACTTACAACCCAGAAGAAACTGGCCTACCTGGGCTTCCAGTGTC
TTGATCACCCACCCTATTCTCCGGATCTGGCCCCGTCGGACTATCCCCTGTTCCCTGGAT
TGAAAAACAATTCACAGTTCGCCATTTTTGTCTGATACGCATGCCATTGCTGCGGAGACC
CAGTCGGACGGAAAACTTTCTGATTTTTTTGAGTGACCTGCAAAAGTTAGTGTTTTGAGC
TTCGTGAGAAGTAAGTTGAATAAACCCCGAGTTTGGTCGCTGTAGCTTGTTACCTTCCTG
GTCAGGCCCTATCAGCACCCCCTTGTACACAACAGAACAAGACAGGCAATGTACTTATAA
CATAACAATGAGATGCGTTAGCGTAATCACTGTTGTCATGGAAAGCTATTAAGTATTAAA
TCTTCAGAGTGTGTGCTTTATTTTTAATGTATGAAAAGCGCATGCGCCGAATTATGTTTC
TACCTCTTGCCTATCTGGCTCTGCCACATTTTCCACATTATCTCATAAACGGCACGGTTT
TCCGAAGAGGGGGATATTGAAAATAAAATGCGTTTTTTATTTTCTCTAAAAATATGCTCA
TTCTAAGAGAAATTCAGCGAGATATTATAAAAAATGTACGCAGGTATTCATATACATTAC
GCGTTATTCCTTCAAACTTTAACAAAACTTGAATTCTCTCGATAGATTTTAATGAAACTT
AAATTTTATCGATAGATTTTAATGGAACATGGATTTCCTCGATAGATTTTAATGAAACTT
AAACTTTGTCGATAGATTTTAATGAAACTTTAATTTTATCAATAGATTTTAACGAAACTT
GGATTTTATCAATATATTTCAATGAAACTTAAATTTTATCGATGAAACCTGAATTTTTTC
GAGAGATTTTAATGAACCTTAAATTCTATTCATATATTTTAATGTAACTTGGATTTTATT
GATAGATTCTCGAAAAATATTCCCATACGAAATTGCATAAAAGTCGGTGCAGTGGTAGCC
GATTTGTTCCATGTGTACAGACGGACGGATATGACGAAGCTAATAGTAGTTTTCGTAATA
TTCCCAACGCGCCTGAAACCTGGTTTACGTTTCTTTAAGAAGTGCGCATATGACCGCTCT
TTCTCGTACAGTCTGTCCTGCTGTCATTGTTACATTTTAACCAGAACTGGAACATATATA
GACGCATTTCATTAAACCTCTCTCCCCATGACGATCAGTAAGCCAATCTCGATTCACGTC
ACGCACACACAGGGTACCGGACAAATTTAAAGGATATCTGAAAGCCTGCCTCATCGTGTC
TTGTGTTTCGTTTCTTAATAGCAAATTTTACAGAAAATAATATAATAGTAATATGGGTTT
ATTATTGCTCATTATGAACGTTCCGCTCCACTTAATAACACGAACTTTTATGTATTTACC
GATTATTTCAATACTGCAAGGTTTATAAAGTGTTTGGCAGAGTTTCAAAGAGATCAGAAC
TGGAAAGGGCTCATAAGACATCCAAGAAATATTGATTAAAAACCCTGACATCATCCGGAA
GAAAGCACCACGTAATTTCAGAAAATAACAACTTTCAACAATATAAACAATGACCTAAGA
AGCATATAATTCATCCTATCTGCATTTAAGGACTGAGTTCCTCATACTTCTCAGGCAACA
CACTGCGTCTCCATACCACTTCATAAATTTAAGATGAGAAATTCCCGCTGGTGTAAACAA
ATCACAAGTAAATACGTTAAATCAGTCACACACAACACCGGTTTTGTAATCAAATGCCTT
TAATAAAGTTGATAAAAACTAGTATTGTGTGCTACTGATTTAATACACACATTTACAAGC
ACATAATGCTGTTTAGGGTAACAATCGCTTTTTATGTGACCAACATAAGTTACGCACTAA
CACTAAGTGTTGCATAATGCTGAGTTTCCTGCTGCTGCAGTGTGTGGTACCAACCAATGT
GCTATCCAGGTTCAAAATAAACGTTTGACATGTTTTATAAGACATTTTCATCTTCATTCC
TCCCATATTTTTTGAAAGAAATTCTACACTTTTTATTTATGGTCGCCTATCTCTAAAAAA
AAGTATGTAACTTTAGTGACGCTGTTTGACGTAGACCCATGAGTGTGGTTCCCTGTCACC
ACCGCTGCAGGAGCTAAATAATATCTATAATACTTGCTACGTA
CACTGCTTCATAGCACGCTGCAGGAGCTAAATAATTTCTATAATACTTGCTCCGTACACT
GCTTCACGGCACGCTGCTGGAGCTAAATAATTTCTATAACACTTGCTCCGTACACTGCTT
CACAGCACGCTGCAGGAGCTAAATAATTTCTATAATACTTGCTCAGTACACTGCTTCAGA
GCACGGTGCAAAAGCTAAATCATTTCTACCCGGTACTTATCTGTACTCAGTTCATAGCCG
CACAAATTCACAATTTACAGAACTTGTCATATTTATTTTATTTTTTTTCAATCTCTTTGC
GCAGCACTTGGAGATGCTTCGTGGAGCACTTGGTGCTCCTAGAACACAGATTTGAGAATA
TCTGCACTAGACCACCGAAGCCGCTAGGGGACGTATGGTACACAGCATTCTACGTAATAC
ACAGTGAGTGTCCAAAACACAATATCACACTCAACCCAGTGGTGATGAAAAGCACTATTG
TGATTTTATTCAGGTTAAAAATAAATACAATACAATACAATACAATACAATACAGTACAA
TACACTGCAATACACTGTGATAAAATACAATACAATACAATACAATACAACGCAATACAA
TACAATACAATACAATACAAGATGATACAATGCAGCGTAATACAACGCAATACAATACAA
TGCAAGACAATACAATACAATACAATATATTGCAGCGCAATACAATGCAATGCAATACAA
TACAATAAAATTTAATACAATACAATGCAGGGCAATGTAATACAATACAATGTAAAAATA
CAATACAATACAATGCAATACAATGCAATACAATAAAATTCAATACAATAAATTACAAGG
CAATACAATACAACACAATACACACCGAACACCTATACTGGATATGGCTTGATACATGAA
AATCCTGCCCTTTGTTGCCTGTTATCTGATTTATTCTTCACCATCCTTGTAAAGCCATAT
TGGATGCCATAGTGCGCTAATATTTCATATGTTACAGATTGTATTGAATTGTTAGTTAAC
CGTTAGCCTACCGAATTAACCGTGTAACGCCGAACCACTTATAAAGACGTAGTGCAGTCA
GACCTGTAACAATTAAAATTCCCAGTAAAAATATGCGTGAAAAGCCAACAAATACACCAA
ATATTGATTCAGTTTATTAATTATGTATGGTATCTCCTACATATTTCGGCCGTATATTTC
CATCTTCAGTGCCATCTGAGAGATGCTCAATTGAGGAGCAGTCGATAGAATATTGTGGTT
GGGCCTGTTGTGTCTAGTGACGTGGTGCGCCGAGCGTACCACGTCACTAGACAAAATGGC
ATTGTAATGCTGAAACATGTTGGAACTGCCATAAGTAATTACTAAAGTGAATGAATAATT
GGTGTATTTGTTGGTTTTCATGCATCCCTTTAAACGTTGAATAAGATCCCATTCGCCATC
CATTACTAGGAGGTATTACTATAATGGTCGTTAGCAGGTTAAGGGTTAATTTAGTCCTTG
GGTTGCATACCTGCATTGACTATGTTAGATAACATCCATCCTTCTGTGTTATGAATATGA
CATACATAAGTAATTACACAGTGTTCAGTCTACCAAACTCAGTTTTTTTATTATTGACAA
CTATTACAGACACAACATGTTTCGGTGTTTTCAAACCACCATCTTCAGGCCTTCTATTGG
TCGAATATTTTACTAGAATGCTACATACAGTAGCCACATATTTCGGAGTTTTCAAACCAC
CTTCTTCAAGACTTTTATTGGACGAATATTTTACTATAATCCTACCTACAGGGTCCACAT
ATTTCGGAGTTTTAAACCGCCATTTTCAGGACTTCTATTAGACGAATATTGTACTAGAAT
GCTACCTACAGAGGCCACATATTTCGGAGTTTTCAAACCACCATCATCAGGACTTCTATT
GGACGAATATTTCATTAGAATCCTACCTACAGGGGCCATATATTTCGTAGTTTTCAAACC
ACCATCTTCAGGACTCCTATTAGACGAATATTGTACTATAATACTACCTACAGCGTCCAC
ATACTTCGGAGTTTTCAAACCGCCATCTTCAGGACTTCTATTGGATGAGTAATTTACTAG
AATCCTACATACATGGTCCACATATTTCGGAATTTTCTAACCGCCATCTTCAGGGCTTCT
ATATTGTCGGCTCTATAAAGTAAAGATAGAGAGAAAGAAAAGG
AGGGTGGTGCAATACAGTGTTGAAGACCTGTCGTATTGCGTATTTGAAGTACTTGCCTGC
TCGGGCCTACGCTATCTGCTGCGGGTAGGAGTGCTGACGTAAGAGAATACACGGTTTTCG
AGCGAAGGAATTCCACTGCTCTCGTTCAAAAAACATCTACTTTATTTAGCTACTCCTACA
CTAACCTATATAATGCTAGGCGACTCCCGTAGAACAAGTTAGGGGTTGCGTCGCTGTATT
ACGCTGGCTTATCAATTTTAACGCACTTTGCTTTAGTTGGCACGTAACTTTCACACGACT
ATTCACTGAGTAAAGATTTTCCACTCACCTGTGATTAAGTAATTAATCCTCATTGCGTGT
GTTAATCCAGTGTGGTTCACTTATAAATGGTTACACTTTTCTATTCACTGCGGGTTAATT
TGGCGTCTATCTAGCACACGTGTTGTACTTTAGCGTATTTAATTAATAATTCCAATTCAA
TCTTTAATTGTTAATCTCGATGTATCAAAACGTTCAACAATAAATTATTAACTGAATTAC
TTAGTTATAAACTTTCAATTTCGTAGTTATAAGACCTAATAAATTGTCGTCCTTAGAGAA
GGTACGATTATTCAGAACATGTTAACGCGTTGAAGACTTGTGGCGGACTCTCTCAAACCG
ACGCTCCTAACATCCGCTCAGCCCATGCTGTCCACCAAGGCAAGCGTCTAATTCAGCATA
ATTCTTGCAAAATCGTGTTTTCCACGGCACGAACAACAACTGGAAACAAGCTCTGGGAAG
TAGCAACTCGGCAATCCCAACTGCTCTACAGGAAGTCTGACTATAGTTTCAACAAACAAG
TGTCTGAAATCTAACTTCTACTGAAACAATTCTACCTGCAAGAAAATTCAAGTAAAACCA
CAAGGTTTAAACAGCGTTATCTGTTACAATATTAATTTAAACCATTCGGCACCCTCCATC
AAAGACCTCATAAAACTGCAAAAACAGCACTTACCCATACGCTCGGTCATAAACTGGAAG
AAAGCCCCAGCTTACAAGCTGACAAAACCTCTAACACAGAGAATAAAAGAGCTGTCTCTC
CTAACATATGCCTTTAACGTGAAGAATTCCACACAACTGATACACGACGTCAAGAAGACC
CCTTTCCAACCATCACACACTCTGGCCACTCTAGACATATCAAACATATCAAACTCCAAC
ATACCACTGACGGAAACCAGACACATCCTGAACCGGTCTCTAGTGAATAACATGGTAGAA
AACAATATTACAAAAGAACTGCTGGCATGGTACGACACCGTCACCGAGCAGAACTTCACG
TTCAAGGAACACACGGACATCCAAACAGACGGACTAGCGATGGGGGCTCCTACATCCAGC
GTCTTATCAAAATTCTTCCTACAACAGATGGAGCACACACACATCCCAAACTTTGCAAGA
AAACACACTCTAGTGAACTACTTTCGATATGTTGACGACATACTCATAATCTTTGACTCT
AAAGCCACTGACATAAAATCCATCCTGATCGAATTCAACGCCATACACCCAAACCTCAAG
TTCACAGCAGAAGTGGAACACAATAACGCGATCAACATCCTGGACACTACCATACAGAAA
ACAAAAAACAACTTAAAGATATCAATCTACAGGAAATGCACGTTTACTAAACCATCATCC
CGTATACCTCAAATCACCCACCACAACACAAACACGCCGCAGGCAGGTTCCTGTATAAGA
GATTGAACACTTACCAACTACAAACAGAAGAATACAAACAAGAAGAAAACCTTATCCACA
ACATATTTCATAGTACCTCCTTTTCTATTCGACCATGTAAGGACCCCTCCAAACAAATAC
AAAAACAATCAACATCCCAACAAACTCCGATCCAGAAGTGAGCTACCTTTACTTACACTG
GTAGAGAGACTAAATACATCACCAGCCACTTCAAGAACTCTAATATAAGAATTTCTTTCC
AAACAAAAACTCCATACTAAACCACATAACAAACCGCAATCACGGCCACAGAGACCCATA
CACTTCCTCAGGAATACACAAGCTGACAAGCCCTGACTGCGGCAAAGCATACGTAGGCCA
AACTGGCGTAATGTTCTCCATAAGTTTCAAAGAACACAAACAAGCCTTCCGTAACAACAG
CCCAACTTTTTTGGATTTATTTTTGCTCCGTGTATTTCACG
CACCACCGTACTGTTCATTTTACCAGTCATCTCACTACCTGCTTCACAAAGTTATCCTAA
ATACCGTACTTCAACACTGCAGCAGTACAGTACACATTTACACACAAACAGTACACAGAA
CAACACAGTGCAGCAGTACAGTACACATTTCACACACAAACAGTACACAGAACAACACAG
TGCAGCAGTACAGTACACATTTACACACAAACAGTACACAGAACAACACAGTGCAGCAGT
ACAGTACACATTTACACACAAACAGTACACAGAACAACACAGTGCAGCAGTACATTACAC
ATTTACACACAAACAGTACACAGAACAACACAGTGCAGCAGTACATTACACATTTACACA
CAAACAGTACACAGAACAACACAGTGCAGCAGTACAGTACAAATTTACACACAAACAGTA
CACAGAACAACACAGTGCAGCAGTACAGTACACATTTACATACAAACAGTACACAGGACA
ACACAGTGCAGCAGTACAGTACACATTTATACACAAACAGTACACACAACAACACAGTGC
AGCAGTACAGTACACATTTACACACAAACAGTACACAGAACAACACAGTGCAGCAGTACA
GTACACATTTACACACAAACAGTACACAGAACAACACAGTACAGCCAGTACAGTACACAT
TTACACACAAACAGTACACAGAACAACACAGTGCAGCAGTACAGTACACATTTACACACA
AACAGTACACAGAACAACACAGTGCAGCAGTACAGTACACATTTACACACAAACAGTACA
CAGAACAACACAGTGCAGCAGTACAGTACACATTTACACACAAACGGTACACAGAACAAC
ACAGTGCAGCAGTACAGTACACATTTACACACAAACAGTACACAGAACAACACAGTGCAG
CAGTACAGTACACATTTACACACAAACAGTACACAGAACAACACAGTGCAGCAGTACAGT
ACACATTTACACACAAACAGTACACAGAATACAGAGAACGGAACATACATAACAATAAAA
AAATTAAACATACATAACAATAAAAATTGAACATACATAACAATAAAAAATTGAATATAC
ATAACAATAAAAAAATTTAACATACATAATAATAAAAAATTGTACATAACAATAAAAAAT
TGAACATACATAACAATAAAAAATTAAACATACATAACAATAAAAATTAAACATACATAA
CAATAAAAATTGAACATACATAACAATAAAAAATTAAACATACATAACAATAAAAAATTA
AACATACATAACAATAAAAATTGAACATACATAACAATAAAAATTAAACATACATAACAA
TAAAAAGTTATACATACATAACAATAAAAAATTGAACATACATAACAATAAAAATTAAAC
ATACATAACAATAAAAAAAGTAATCAAAATCAAGCCGGAACACGTGACTGTACTGCATTT
GGCAACTCTGCTTGCACAACCACGCCATGACCCACACTACGTTAATATACAGCATGGCGC
ACGAGATGTCATACCATTTTATCATACCATTAAAATTGTAACATCATAGTATCGATGTTG
CAAACGTGCGTGTGAATGTTGAGGTTCATTGAAAATCCGATAGATGTCACCAGTTTGTAA
AATGGCGGACAACGGACGGTTGACTGTAGACCGAAATGCTTTTGTAATAATAAAACTGTG
TAACGTGTCCAATCAATGGTATGACATTTCGTGCGCCAACCTGTCTCATTTTTGCTATAT
ACAGGGTTATTCATAAGTCCTTCCGGGATTTCCGAAATCGACTGCGCAACAACCAAGACA
GACACGGCAGAAAGGAGCATATCAATAGGTAGAGAATCTCTCCAAGTTTTTTTTTGTACT
AGGGGCCTTGACGTACTTGCAGATTCCACCGCTAGGGGGTAGTCGTGACGAAAAATGGCG
TTCACAGTGAATAAGAAAGCGTTCTGTTTCTTGGAATTTGCCAAAACTGAGTCAATTGTG
ACAGTGCAACGGAGGTTTAGGATCATGTACCCCTAGTACAAAAAAACTTGGAGATATTCT
CTGCCTATTGATATGCTCCTTTATATCGTGTCTGTCTTGGTTGTTGCGCAGTCGAGTTCG
GAAATCCCGGAGGGACTTATGTATAACCCTTGTATATACAGGGTGTCAACACGTAACCGA
ACGAAGCACAATTGCAACACAAATACCATATGTTCGTTTTG
GGCTCTGAAAAAGCAAATTCCAACGACACACGCAATACATCGATGGAAAACCACAATGAT
TGAGACAAATACTAAATTTTCGTTTTTGGCCCTGAAAAGCAAATTCCCAACGACACACGC
AATAAATCGATGGAAAACGACAATGGTTGAGACCCAAATACCATATGTTCGTTTTGGGGT
CTGAAAAGCTAATTCCAACGACACTCGCAATACATCGATGGAAAACCACAATGATTGAGA
CATAAATCCTAATGTTCGTTTTGGGATATGAAAAGCAAATTTCCAACGACACAGGCAATA
CATCGATGGAAAACCACATTGGTTGCGACACAAATACCATATGTTCGTTTTGGGCTCTGA
AAAGCAAATTCCCAACGACACACGCAATACATCGATGGAAAACCACAATGATTGAGACAT
AAATACTAAATGTTCGTTTTGGGCTCTGAAAAGCAAATTCCCAACAACACACGCAATAAA
TCGATGGAAAAACACAATGGTTGAGAGACAAATACCATATGTCGTTTTGGACTCTGAAAA
GCAAATTGTCAACGACACACGCAATACATCGATGAAAAACCAGAATGGTTGAGACGAAAA
AACCATACGTTAGTTTTGGGCTCTGAAAAACAAATTCCCAACGACACACAAAATACATCG
ATGGAAAACCACAATGGTTGAGATACAATTACCATATGTCAATTTTGGTCTCTGAAAAGC
AAATTCCCAACGACAGACACAATAAATGGGTGGAAAACCCCAATGGTAGAGACACAAATA
CTATATGTTCGTTTTGGGCTCTGAAAAGCAAATTATCAACGACACACGCATTACATCGAA
AGAAAAGCACTATGGTTGAGACACAAATACCATAAGTTCGTTTTGGGCTCTGAAAAGCAA
TTTCCCAACGACACACAAAATACATCGATGGAAAACCACAATGGTTGAGACACAATTACC
ATATGTCAGTTTTAATCTCTGAAAAGCAAATTCCCAACGACACACGCAATACATCGATGA
AAAACCAGAATGGTCGAGACACAAATACTATATGTTCGTTTTGGGCTCTGAAAAGCAAAT
TATCAACGACACACGCATTACATCGAAAGTAAAGCTCTATGGTTGAGACACAAATACCAT
ATGTTCGTTTTGGGCTCTGAAAAGCAAATTCTCAACGACAAACGCATTACATCGATGGAA
AACCACAATGGTTGAGAGCCACATACCATATGTTCGTTTGGGGCTATGAAAAGGAATTTC
CTAACGACACCCCCAATACATCGATGGAAAACCAAAATGGTCGAGACGCAAATACCATAT
GTTACTTTTGGGCTCTGAAAAGCAAATTCCCAACGACACACGCAATACATCGATGTAGAA
CCACAATGGTTGAAACACAAGTATCATATGTTCGTTATGGTCTCTGAAAAGCAAATTCCC
AACGACACTCCTAATAAATCGATGGAAAACCACAATGGTTGAGACACATATACCGTATGT
TCGTTTTGGGCTTTGAAAAGCAAATTCCCAACGACACACGCTATACATCGATGGAAAACC
ACAATGGTTGAGACACAAAAACTATATGTTCGTTTTGGGCTCTGAAAAGCAAATTATTAA
CGACACACGCATTACATCGAAGGAAAAGCACTATGGTTGAGACACAAATAATATATGTTC
CTTTTGGGCTCTGAAAAGCAATTTCCCAACGACACACGCAATACATCGTTGGAAAACCAC
AATGGTCGAGACACAAATACTATATATGTTCGTTTTGGGCTCTGAAAAGCAAATTGTCAA
CGACACACGCATTACATCGATGGAAAATCACAATGGTTAAGACACAAATACCATATGTTC
GTTTTGGGCTCTGAAAAGCAATTTCCCCACGACACAGGCAATACATCGATTGAAAACCAC
AATGGTCGAGACACAAATACCGTATGTTCGTTTTGGGCTCTCAAAAGCAAATTGTCAACG
ACACTCGCAATACATCCATGGAAAACCACAATGGTTGAGACACAAATACCATATGTTCGT
TTTGGGCTCTGAAAAGCAAATTGTCAACGACACACACAATACATCGATGGAAAACCAGAA
TGGTCGAGACACAAATACCATATGTTCGTTTTGGGCTCTGAAAGGCAAATTATCAACGAC
ACACGCATTACATCGAAGCACTAGGTAAATTGAAATTGTGT
GGCGTCCAGTGGGAAAGTACAGGGCTGTTGGTCTTCACATAGCCGCTAGCTAAATTGAAA
TTCTGTGGCCTACAGGGGAAAGTACAGGGCAGTGGTTTTTCACATAGCATTAGGGCCTAA
AATATATGTTTAATAGCACAACTATGACTCTCGATTTGATTTAACATCTAAAAGAAATAA
GTGCCAATAATATATCCTTGGGAAAATTCGGCCGGTTCTGTAGGGCTGACAACCTTTCCA
CCTTCATGTGCCGATTTTCTTAAAATCTGGTAGCCCCAGCTCCTGGAACTCTAAAGGGTC
TGTCATGGGCTGTATTATTATTATTATTGGTTATTATTATTATTATTATTATTATTATTA
TTTTCTCTGGCTCTGCAGCCCAGCTCGTGCCTATGGCCTCCTCTTTCACGATGTTTCTTA
ATCAAACCTAACGACGGGCCATATTCTGTAGGACTCCTCTGGACGAGTGATCGGCCCGAC
CCAGAGACTACTATCTGACAACAAACAACCCACACAACAGACAAACATCCCTGCTCCCGG
TGGGATTCGAACCCACGATCGCAGCAGGCGAGCGGCCGTCGACCTACGCCTTAGACCGCA
CGGCCACTGGGACCGGCTCTTAAGCCGGTAATGGGTTTTTTAACATTTAAATTAACAATA
TGGTACATATATGTATCATTATATACAGGGTGATTCAGGAGAAATCTGCAATAATTTGGG
AAATGATAGTATGTGTGATTCTAAGCAAAAAGTTCATATGAACTTGGGTACGGTTTTGAA
CGTTTATGGAAGATACGGACCATCGGTTCGAAATCCCTAGTAAAAAATCTCGTCCATTAT
ACAGGGTGATTCAGGAGAAATATGCAATACTTTGGTAAATTATAGTATGTGTGATTCTAA
GCAAAAATGTTCATATGAACATGGGTCCGATTTTTAATGGTTACGGAAAATACTGGGCAT
CCGTTCAAAATCCCCACTAAAAAATCTCGCCCATTATAACAGGATGATTCAGGAGAAATC
TTGCAATAGTTTGGAAAATGACAGTATGTGTGATTCTAAGCAAAAACGTTCATATGAACA
TGGGTCCGATTTCGAACCTTTACCGAGATATGGTAAAAGGAAAATTCAGACCATCCGTTC
CAAAATCGGACCTAGGTCCATATGAACTCTTTTGCTTAGAATCACACATACTATTCTTTT
CCCAAAGTATGCAAGATTTCACCTGAACTCACCCTGTTTATATATATATATATATATATA
TATATATATATATATATATATATATTCCTTCACCGTTTGGCTCCCGAAAATGTTCATCCC
ATTCTACTTCCAATAAAACTCCGTTATGGTAGCTGATTCCGGGAAAAATATTACGAGAGA
TGAGCGAACCTTCAGGTCTGAGAAGATATACAAAGTGCGACCCAAAAGTTTTTAGACGAG
TTGTTATTTTTTTTTCGACGCAGAAGGTGTAATTGATCGATAGTTTGTCCCTGAAGGGCA
GAAAGTAAATGCAGAATTCTACGTGGGTGTTTTGGATCGGCTACTGAAGAGAATTGAACG
CGTTAGAACGATCAAATTCCAACCCATTGAGTGGGTTCTACTTCACAATAACGCGCCATC
TCATAACGTTCCAATTGTACAGAATTTTCTGGCGAACAGGAACGTTGCTCTTCTCCACCA
TCAAGAGTGCATACCAATGTGAGCTGTCGTTCCACCATGTTCTCGTTGTGTTGGGCTGTC
GATGATCAGATGTACCAAATTGCTTACTCAGTTGTAACATACAATAAAAAGCAAACACCA
CTGAATGAGTTGGGGCGTGTTTACAGCGCGGTAGGGATTGATTTCTTACATTAAAAAATT
TATAAACCGTAGAGGAAAGTGTTTACAGCGCGGTACGGAATGATTGCTTACATAAAGCAG
ATATAACCGTGGTGGGAAGTTTTTAGAGCGGGGTAACGAACTGATTGCTTATATAAAGCG
GATTTATAACCGAGGTTGAAAGTAGCTTATCAGCGCGGTACAAACTGATTTCTTATAAGA
AAGCAGGTTTATAACCTCTGGTAGATAGTGTTTAAAGCGCGTGTAAGGACTGATTGTTAT
ATAAAGCAGATTTATGGACCGAGTTGGAATGTGGCTTGACAGCGCGGTACAGCAACAACG
CACCGAACGCAGCCACACCTGGTGTATTTGTTGGTTTTCC
ACCCATATATTAACGAAATGCACGGTTCAAGGAGCAAAATACCCAGTAAAAAAATCTCGT
CAGGCAGCGTTGCGCGGAGGGGTTTAATTCCGTCTTTTAAAGGTTAAACCCCATGGAAGT
TAAAGAGTTTGGCCTTTTTTAAACAAAAGACCACACTCTACATTTCCCTCCGCCCCGGGC
TGTGACAAGAGGTCGACTTGTAAATGAAGCGCAAGTTCTTATTAGTGGACCCCCCCCCCC
ACTCCAACTCCCCTTTTACGCTTTTCATGTAACGTACAATGCAGCCATGAGGTAAGGTTC
TGATCTTAAACTCTCTGCGCAAAGATTGTAATGAATTTTTGACATATAAGCTTTTGAGTT
TTAAAGACCAAGATATATAGAACTATAATTTTGCCTGTTGTTTTGTATGGGTGTGAAACT
TGGGTCTAAGAGGGACGAGGTGACAGGGGATTGGAAAAGTTACATAACGAGAAGCTGAAT
GATCTGTATTCCTTACCCAATATTGTGCGGGTGGTTAAATCGAGAAAAATGAGATGGGCG
GGGCATGTGGCGCGTATGGAGGAGGAGAGAGGGGTGCACAGGGGGTTGGTGGGGAAACCT
GAGGGAAAGAGGCCTTTGGGGAGACCCAGACTTAGATGGGAGTATAATATTAAGATGGAT
CTTCAGGAAGTTGAAGGGAGTCTTGGGGACTGGATAGAGTTGGCTCAGGATAGGCACGGG
TGGTGGACACTTGTGAGTACGGTAATGAACTTTCGGCTTCCATAAAAATGAGGGGAATTT
CTTGACTAGCTGCAAAGACTGGTCGGCTTTTCAAGAAGGACTCTGCTCCATGGACTATGT
AAGTAAGTAACCTTTTTAGTTTTATGTTCTGAACAGTCAGTATATAAAACATGCTACCGT
TCTTACAGTGGCTTAGCTAACCGGACGTACTTCCTCCCCGCTCACAATTATTACAGAAAT
TATGTTTTGTTCACCGTTCATCTCGCTATATGCGTGTAATGAAACCAACTTCGTTCACTA
TTCATCTTCATTTTATTCCGTAAATATACCTCTACATGTTTCGGGCTTGCTAGTTGCCCA
TCATCAGGAGGTAACAATGTACGTAGGTGAGTCAAATGAAAACCTTAAATACTTATTAAT
TTATTAAATATTAAATATTTATAGAACTGCAAAAAATTATAGACGATATGGTGTGCTGAT
CCATGGCTCATATCCAGATGTGCGGCTATTTCGTTCACTGTTACGCGGTGATTTTCCTGC
ACGATGGCTTCAACTGCCGCAATGGCCTCTGGTGTCACTACTCGCTGTGCCTGACCAGGT
CGAGGAGAGTCTTTTGCAGAACAAATGCCGTTCATGAAATTCTTAGTCCACTCATACACT
TGCTGTAGTGACAGACATGCATCACCTTACTGAACTTTCATTCTTCGATGAATTTCGTTG
GGTTTCATTCCTTCAGTATTTAAAAAACGGATGGTGCATGTTGCACGCGGAGCCGCCATC
TTTACACCAATACTGCGCCGTCATGTTGCATCCCTGCATCATACTGCCACCTGTCAGTCA
CATTTCAAACCATGAGTATTTTTGTTGTCAACTTACAAGACAATCGAGCTGTGTTTCGAA
TTTTTATAGCACTTTTAAAGTTTTCATTTGACTCTCCCTCGTATATACTCGTATGTGTGT
GTGTGTGTGTGTGTGTGTGGTGTGTGTGTGTGTAACAAATGTCACGTGTTGTACCTGTAT
TAGCCGACTGTCGCATCTCAACCAGGCCAGATGACAGTCAACTAAAACCTACAACACGTA
CCAATTGTTGCATATATACTTTGTTACCTCCTGATGATGGGCATCTAGCAAGCCCGAAAC
ATGTAGAAGTATCTTGATATGATCCATCCCGTTGTGTGTTGAAACAATAGTAACAAAGTA
GAACCCGTCAAACACAACACTTTGCATGGATTAAGATGTGAGCAAAGGTGGCTACACGTT
TCGGCCTAACATTTCATGTATTTTGCTGATCAATTGTTCCATAATGAATGACCTGATGAT
GGCCTCTTGCTAGGCCGAAACATGTAGCCAACTTTGCTCACA
>mite|17742|79|90|135|146|t7|85|m1|ave_score:0.614806
ATATACGGGCATCAGAACATGCTATGTCATTAATATGCACAAGGTCATAGAAGAATTTTA
ATATGACCTAATAGGACCTAATCTAATAAAAGTCTTTATATATACATTTTTAATTAATTA
GGTCTTATAATTTTATATTTATGTTCTAATTCTATCAAAAGAGTAACTGTACACTAGGGA
CCCATTAG
>mite|17987|1773|1783|1834|1844|t4|1778|m1|ave_score:0.678183
GTGAACGAGGAGGCCATAACACGCGCTGGGCTGCAGTGCCAGAGAAAATAAAACAAATAA
TATTCTCTAGAAAATAAAAACAAAAAATATTTCTATAGAAAATAAAAACAAATAATATTT
CTCTAGAAAATAATAACAAATAATATTTCTCTAGAAAATAAAAACAAATAATATTTCTCT
AGAAAATAAAAA

Looks like some header lines are missing?

Sincerely,

Cong

how are we going to use your Tool

We need the instruction how to compile and use it , if you need the researchers to use your tool and cite it

how to parse the output result

Hi,
Through I see the readme, I counld not know which the exact position of MITE, and the header is like this: mite|1|170025|170037|170078|170090|t2|170026|m1|ave_score:0.711664, how can I get the MITE position?
I waiting for your reply, thank you.

manual

Hi,

Could you please provide more info on how to install and run? After compiling it, I had miteFinderTest. However, miteFinderTest seems to be running forever without producing any results.

below is the code I used
/scratch/luohao/software/miteFinder/miteFinderTest -input bb.fa -threshold 0.5 -output bb

Thanks!

Issue in detection

Dear Jialu Hu,
Greetings!
I am using miteFinder in Transposon Ulitimate, but it generates 0 KB resutls.
Then when I run it alone it generates 2.7 MB results of 2.Gb size.
could you give me some suggestions?

with kind regards

Ramky

About pattern_scoring.txt

Hello

Thank you so much for developing this software.

I am trying to run the inicial command, however, I will like to know more about the pattern_scoring.txt

What is this file and can we used for any sample?

Sincerely,
Loi

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