einverted |
Please help by correcting and extending the Wiki pages.
einverted finds inverted repeats (stem loops) in nucleotide sequences. It identifies regions of local alignment of the input sequence and its reverse complement that exceed a threshold score. The alignments may include a proportion of mismatches and gaps, which correspond to bulges in the stem loop. One or more sequences are read and a file with the sequence(s) (without gap characters) of the inverted repeat regions is written. It can find multiple inverted repeats in a sequence. Only non-overlapping matches are reported.
einverted uses dynamic programming and thus is guaranteed to find optimal, local alignments between the sequence and its reverse complement. Matched bases contribute positively to the score whereas gaps and mismatches are penalised. The score for a local alignment is the sum of the values of each match, minus penalties for mismatches and gap insertion. Any region whose score exceeds the threshold is reported. The gap penalty, match score and mismatch score, and the threshold score for reporting regions, are all user-specified.
% einverted tembl:d00596 Finds inverted repeats in nucleotide sequences Gap penalty [12]: Minimum score threshold [50]: Match score [3]: Mismatch score [-4]: Sanger Centre program inverted output file [d00596.inv]: File for sequence of regions of inverted repeats. [d00596.fasta]: |
Go to the input files for this example
Go to the output files for this example
Finds inverted repeats in nucleotide sequences Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] seqall Nucleotide sequence(s) filename and optional format, or reference (input USA) -gap integer [12] Gap penalty (Integer 0 or more) -threshold integer [50] Minimum score threshold (Integer 0 or more) -match integer [3] Match score (Integer 0 or more) -mismatch integer [-4] Mismatch score (Integer up to 0) [-outfile] outfile [*.einverted] Sanger Centre program inverted output file [-outseq] seqout [ |
Qualifier | Type | Description | Allowed values | Default |
---|---|---|---|---|
Standard (Mandatory) qualifiers | ||||
[-sequence] (Parameter 1) |
seqall | Nucleotide sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required |
-gap | integer | Gap penalty | Integer 0 or more | 12 |
-threshold | integer | Minimum score threshold | Integer 0 or more | 50 |
-match | integer | Match score | Integer 0 or more | 3 |
-mismatch | integer | Mismatch score | Integer up to 0 | -4 |
[-outfile] (Parameter 2) |
outfile | Sanger Centre program inverted output file | Output file | <*>.einverted |
[-outseq] (Parameter 3) |
seqout | The sequence of the inverted repeat regions without gap characters. | Writeable sequence | <*>.format |
Additional (Optional) qualifiers | ||||
-maxrepeat | integer | Maximum separation between the start of repeat and the end of the inverted repeat. | Integer 0 or more | 2000 |
Advanced (Unprompted) qualifiers | ||||
(none) | ||||
Associated qualifiers | ||||
"-sequence" associated seqall qualifiers | ||||
-sbegin1 -sbegin_sequence |
integer | Start of each sequence to be used | Any integer value | 0 |
-send1 -send_sequence |
integer | End of each sequence to be used | Any integer value | 0 |
-sreverse1 -sreverse_sequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
-sask1 -sask_sequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
-snucleotide1 -snucleotide_sequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N |
-sprotein1 -sprotein_sequence |
boolean | Sequence is protein | Boolean value Yes/No | N |
-slower1 -slower_sequence |
boolean | Make lower case | Boolean value Yes/No | N |
-supper1 -supper_sequence |
boolean | Make upper case | Boolean value Yes/No | N |
-sformat1 -sformat_sequence |
string | Input sequence format | Any string | |
-sdbname1 -sdbname_sequence |
string | Database name | Any string | |
-sid1 -sid_sequence |
string | Entryname | Any string | |
-ufo1 -ufo_sequence |
string | UFO features | Any string | |
-fformat1 -fformat_sequence |
string | Features format | Any string | |
-fopenfile1 -fopenfile_sequence |
string | Features file name | Any string | |
"-outfile" associated outfile qualifiers | ||||
-odirectory2 -odirectory_outfile |
string | Output directory | Any string | |
"-outseq" associated seqout qualifiers | ||||
-osformat3 -osformat_outseq |
string | Output seq format | Any string | |
-osextension3 -osextension_outseq |
string | File name extension | Any string | |
-osname3 -osname_outseq |
string | Base file name | Any string | |
-osdirectory3 -osdirectory_outseq |
string | Output directory | Any string | |
-osdbname3 -osdbname_outseq |
string | Database name to add | Any string | |
-ossingle3 -ossingle_outseq |
boolean | Separate file for each entry | Boolean value Yes/No | N |
-oufo3 -oufo_outseq |
string | UFO features | Any string | |
-offormat3 -offormat_outseq |
string | Features format | Any string | |
-ofname3 -ofname_outseq |
string | Features file name | Any string | |
-ofdirectory3 -ofdirectory_outseq |
string | Output directory | Any string | |
General qualifiers | ||||
-auto | boolean | Turn off prompts | Boolean value Yes/No | N |
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N |
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N |
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N |
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N |
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y |
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N |
-warning | boolean | Report warnings | Boolean value Yes/No | Y |
-error | boolean | Report errors | Boolean value Yes/No | Y |
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y |
-die | boolean | Report dying program messages | Boolean value Yes/No | Y |
-version | boolean | Report version number and exit | Boolean value Yes/No | N |
ID D00596; SV 1; linear; genomic DNA; STD; HUM; 18596 BP. XX AC D00596; XX DT 17-JUL-1991 (Rel. 28, Created) DT 07-DEC-2007 (Rel. 94, Last updated, Version 6) XX DE Homo sapiens gene for thymidylate synthase, complete cds. XX KW . XX OS Homo sapiens (human) OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; OC Homo. XX RN [1] RP 1-18596 RX PUBMED; 2243092. RA Kaneda S., Nalbantoglu J., Takeishi K., Shimizu K., Gotoh O., Seno T., RA Ayusawa D.; RT "Structural and functional analysis of the human thymidylate synthase RT gene"; RL J. Biol. Chem. 265(33):20277-20284(1990). XX DR GDB; 163670. DR GDB; 182340. XX CC These data kindly submitted in computer readable form by: CC Sumiko Kaneda CC National Institute of Genetics CC 1111 Yata CC Mishima 411 CC Japan XX FH Key Location/Qualifiers FH FT source 1..18596 FT /organism="Homo sapiens" FT /chromosome="18" FT /map="18p11.32" FT /mol_type="genomic DNA" FT /clone="lambdaHTS-1 and lambdaHTS-3" FT /db_xref="taxon:9606" FT repeat_region 1..148 FT /rpt_family="Alu" FT repeat_region 202..477 FT /rpt_family="Alu" FT prim_transcript 822..16246 FT /note="thymidylate synthase mRNA and introns" [Part of this file has been deleted for brevity] ttttgttttt agcttcagcg agaacccaga cctttcccaa agctcaggat tcttcgaaaa 15660 gttgagaaaa ttgatgactt caaagctgaa gactttcaga ttgaagggta caatccgcat 15720 ccaactatta aaatggaaat ggctgtttag ggtgctttca aaggagctcg aaggatattg 15780 tcagtcttta ggggttgggc tggatgccga ggtaaaagtt ctttttgctc taaaagaaaa 15840 aggaactagg tcaaaaatct gtccgtgacc tatcagttat taatttttaa ggatgttgcc 15900 actggcaaat gtaactgtgc cagttctttc cataataaaa ggctttgagt taactcactg 15960 agggtatctg acaatgctga ggttatgaac aaagtgagga gaatgaaatg tatgtgctct 16020 tagcaaaaac atgtatgtgc atttcaatcc cacgtactta taaagaaggt tggtgaattt 16080 cacaagctat ttttggaata tttttagaat attttaagaa tttcacaagc tattccctca 16140 aatctgaggg agctgagtaa caccatcgat catgatgtag agtgtggtta tgaactttaa 16200 agttatagtt gttttatatg ttgctataat aaagaagtgt tctgcattcg tccacgcttt 16260 gttcattctg tactgccact tatctgctca gttccttcct aaaatagatt aaagaactct 16320 ccttaagtaa acatgtgctg tattctggtt tggatgctac ttaaaagagt atattttaga 16380 aataatagtg aatatatttt gccctatttt tctcatttta actgcatctt atcctcaaaa 16440 tataatgacc atttaggata gagttttttt tttttttttt taaactttta taaccttaaa 16500 gggttatttt aaaataatct atggactacc attttgccct cattagcttc agcatggtgt 16560 gacttctcta ataatatgct tagattaagc aaggaaaaga tgcaaaacca cttcggggtt 16620 aatcagtgaa atatttttcc cttcgttgca taccagatac ccccggtgtt gcacgactat 16680 ttttattctg ctaatttatg acaagtgtta aacagaacaa ggaattattc caacaagtta 16740 tgcaacatgt tgcttatttt caaattacag tttaatgtct aggtgccagc ccttgatata 16800 gctatttttg taagaacatc ctcctggact ttgggttagt taaatctaaa cttatttaag 16860 gattaagtag gataacgtgc attgatttgc taaaagaatc aagtaataat tacttagctg 16920 attcctgagg gtggtatgac ttctagctga actcatcttg atcggtagga ttttttaaat 16980 ccatttttgt aaaactattt ccaagaaatt ttaagccctt tcacttcaga aagaaaaaag 17040 ttgttggggc tgagcactta attttcttga gcaggaagga gtttcttcca aacttcacca 17100 tctggagact ggtgtttctt tacagattcc tccttcattt ctgttgagta gccgggatcc 17160 tatcaaagac caaaaaaatg agtcctgtta acaaccacct ggaacaaaaa cagattttat 17220 gcatttatgc tgctccaaga aatgctttta cgtctaagcc agaggcaatt aattaatttt 17280 tttttttttg acatggagtc actgtccgtt gcccaggctg cagtgcagtg gcgcaatctt 17340 ggctcactgc aacctccacc tcccaggttc aagtgattct cctgcctcag cctcccatgt 17400 agctgggatc acaggcacct gccaccatgc ccggctaatt ttttgtattt tttgtagaga 17460 cagggtttca ccatgttggc caggctggtc tcaaacacct gacctcaaat gatccacctg 17520 cctcagcctc ccaaagtgtt gggattacag gcgtaagcca ccatgcccag ccctgaatta 17580 atatttttaa aataagtttg gagactgttg gaaataatag ggcagaggaa catattttac 17640 tggctacttg ccagagttag ttaactcatc aaactctttg ataatagttt gacctctgtt 17700 ggtgaaaatg agccatgatc tcttgaacat gatcagaata aatgccccag ccacacaatt 17760 gtagtccaaa ctttttaggt cactaacttg ctagatggtg ccaggttttt ttgcacaagg 17820 agtgcaaatg ttaagatctc cactagtgag gaaaggctag tattacagaa gccttgtcag 17880 aggcaattga acctccaagc cctggccctc aggcctgagg attttgatac agacaaactg 17940 aagaaccgtt tgttagtgga tattgcaaac aaacaggagt caaagcttgg tgctccacag 18000 tctagttcac gagacaggcg tggcagtggc tggcagcatc tcttctcaca ggggccctca 18060 ggcacagctt accttgggag gcatgtagga agcccgctgg atcatcacgg gatacttgaa 18120 atgctcatgc aggtggtcaa catactcaca caccctagga ggagggaatc agatcggggc 18180 aatgatgcct gaagtcagat tattcacgtg gtgctaactt aaagcagaag gagcgagtac 18240 cactcaattg acagtgttgg ccaaggctta gctgtgttac catgcgtttc taggcaagtc 18300 cctaaacctc tgtgcctcag gtccttttct tctaaaatat agcaatgtga ggtggggact 18360 ttgatgacat gaacacacga agtccctctg agaggttttg tggtgccctt taaaagggat 18420 caattcagac tctgtaaata tccagaatta tttgggttcc tctggtcaaa agtcagatga 18480 atagattaaa atcaccacat tttgtgatct atttttcaag aagcgtttgt attttttcat 18540 atggctgcag cagctgccag gggcttgggg tttttttggc aggtagggtt gggagg 18596 // |
>D00596_13_142 gctacgcgagaggctgaggcagcagaattacttgaacccaggaggcggaggttgcagtga gccgagatcgcgccactgcactccagcctgggtgagagagcgagactctgtctcaaaaaa aaaaaaaaaa >D00596_199_328 ttttttttttttttttttgggacagtcttgctctgtcgcccaggctggagtacaatggtc ggatcttggctcactgcaacctctgcctcccaggttcaagcaattcttctgcctcagcct cccaagtagc >D00596_12128_12301 agaggatttttttttttttttttttttttgagacagagttttgctctgttgcccaggctg gaatgcaacggcgtgatcttggctcactgtaacctctgcctcctgggttcgagtgattct cctgcctcagcctccaagtagctgggattacagcatgtgccaccatgcctggct >D00596_12573_12749 agccaggtgtggtggctcacacctgtaattccaacaactccagaggccaaggcgagagga tcatttgaacccacggaatttgaggctgtagtgagtcatgatcacgccattgcactccat cctgggcaacagagtgagaccctgaatatttaaaaacaacaacaacaacaaaactct >D00596_12246_12296 ctcctgcctcagcctccaagtagctgggattacagcatgtgccaccatgcc >D00596_13886_13938 ggtatggtggctcatgcctgtaatcccagcactttggaagactgagacaggag >D00596_13884_13949 tgggtatggtggctcatgcctgtaatcccagcactttggaagactgagacaggagcaatt gcttga >D00596_14628_14692 tcaagcaattcttctgcctcagcctcccaggtagctgggattacaggcacatgccaccac accca |
D00596: Score 236: 108/130 ( 83%) matches, 0 gaps 13 gctacgcgagaggctgaggcagcagaattacttgaacccaggaggcggaggttgcagtgagccgagatcgcgccactgcactccagcctgggtgagagagcgagactctgtctcaaaaaaaaaaaaaaaa 142 ||||| | ||||||||||||| |||||| |||||||| |||||| |||||||||||||||| ||||| ||| || ||||||||||||| || ||||| ||||| | | |||||||||||||||| 328 cgatgaaccctccgactccgtcttcttaacgaacttggaccctccgtctccaacgtcactcggttctaggctggtaacatgaggtcggacccgctgtctcgttctgacagggtttttttttttttttttt 199 D00596: Score 164: 128/174 ( 73%) matches, 3 gaps 12128 agaggatttttttttttttttttttttttgagacagagttttgctctgttgcccaggctggaatgcaacggcgtgatcttggctcactgtaacctctgcctcc-tgggttcgagtgattctcctgcctcagcctc-caagtagctgggattaca-gcatgtgccaccatgcctggct 12301 |||| || || || || || ||||| | ||| || | |||||||||||||| |||| ||||| ||||||||| || |||||| | |||| ||| ||||||| | |||| ||| |||| ||||| ||| | ||| |||||| | || ||||||| ||||||| 12749 tctcaaaacaacaacaacaacaaaaatttataagtcccagagtgagacaacgggtcctacctcacgttaccgcactagtactgagtgatgtcggagtttaaggcacccaagtttactaggagagcggaaccggagacctcaacaaccttaatgtccacactcggtggtgtggaccga 12573 D00596: Score 80: 44/51 ( 86%) matches, 2 gaps 12246 ctcctgcctcag-cctccaagtagctgggattaca-gcatgtgccaccatgcc 12296 |||||| ||||| | ||||| |||||||||||| ||||| |||||||| || 13938 gaggacagagtcagaaggtttcacgaccctaatgtccgtactcggtggtatgg 13886 D00596: Score 99: 53/65 ( 81%) matches, 1 gaps 13884 tgggtatggtggctcatgcctgtaatcccagcactttggaagactgagacaggagcaattgcttga 13949 ||||| ||||||| |||||||||||||||| ||| || ||||| ||| || |||||||||| 14692 acccacaccaccgtacacggacattagggtcgatggaccctccgactccgtcttc-ttaacgaact 14628 |
The original "inverted" program (from which einverted was derived) was used to annotate the nematode genome. Excluding overlapping repeats saved problems with simple repeat sequences in this genome.
einverted will find optimal alignments but is slower than heuristic methods such as BLAST.
Sometimes you can find repeats using the program palindrome that you can't find with einverted using the default parameters.This is not due to a problem with either program. It is simply because some of the shortest repeats that you find with palindrome's default parameter values are below einverted's default cutoff score - you should decrease the 'Minimum score threshold' to see them.
For example, when palindrome is run with 'em:x65921', it finds the repeat:
64 aaaactaaggc 74 ||||||||||| 98 ttttgattccg 88
einverted will not report this as its score is 33 (11 bases scoring 3 each, no mismatches or gaps) which is below the default score cutoff of 50.
If einverted is run as:
% einverted em:x65921 -threshold 30
then it will find it:
Score 33: 11/11 (100%) matches, 0 gaps 64 aaaactaaggc 74 ||||||||||| 98 ttttgattccg 88
Anything can be considered to be a repeat if you set the score threshold low enough!
einverted does not report overlapping matches.
Program name | Description |
---|---|
banana | Plot bending and curvature data for B-DNA |
btwisted | Calculate the twisting in a B-DNA sequence |
equicktandem | Finds tandem repeats in nucleotide sequences |
etandem | Finds tandem repeats in a nucleotide sequence |
palindrome | Finds inverted repeats in nucleotide sequence(s) |
sirna | Finds siRNA duplexes in mRNA |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
This application was modified for inclusion in EMBOSS by
Peter Rice
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.