AUTHORS: I.A.Shahmuradov & V.V.Solovyev
LAST UPDATE: 15 Novembef 2013
VERSION: 5.2013
ACCESS: http://softberry.com
ACTION: Search for statistically nonrandom and conservative motifs of human/animal and plant transcription Regulatory Elements (REs) available in both of aligned orthologous/homologous DNA sequences.
SEARCH CONDITION:
(1) Expected Mean Numbers of any regulatory motif found must be less than a given number (default: 0.05).
(2) Homology Level of any motif in one sequence with the corresponding area of another sequence (in relation to ALIGNMENT) must be higher than a given level (default: 80%).
As NsiteH and NsiteM programs, Nsite is based on the previously proposed real site and/or their IUPAC consensus based probabilistic approach of searching for putative REs in nucleotide sequences and statistically estimating motifs found (Shahmuradov et al., Genetika (Russ.), 1986, 22, 357-367; Solovyev,V.V. and Kolchanov,N.A. In: "Computer analysis of genetic macromolecules. Structure, Function and Evolution", World Scientific, 1993,16-20).
The main features of the approach are the follows:
(i) RE may consist of a single box (a continuous DNA segment) or two boxes,
spaced by some DNA sequence, where only length, but not nucleotide content, of this spacer is important
for functioning of such a composite site.
(ii) A real RE or its IUPAC consensus contains both variable positions
(where the presence of a certain group of nucleotides is permissible), and strictly conserved positions
(where a strong identity between real site/consensus and predicted motif is required).
(iii) The nonequivalence of these positions should be taken into
account, i.e., complete homology at conserved positions is needed, and a violation of homology
in the variable positions should be permissible.
(iv) The homology between the RE and motif on query DNA sequence may a
chance happening, therefore, estimation of its statistical significance is of major importance.
A conclusion on the functional significance of the revealed homology can be reached, only if the
homology is significantly nonrandom, i.e., the homology is not a chance event.
(v) Characteristics such as nucleotide frequencies should not be used
when describing the consensus because of its small size. Instead, one should use estimates based on
the number of nucleotides of various types in the consensus.
(vi) Although all available databases on REs usually annotate a fixed
distance between two boxes of composite elements, some variability of the spacer length, seems, to
have a place. Therefore, a search algorithm for composite REs should allow some limited flexibility
in the sense of spacer length, relaying on both the known experimental data and theoretical assumption.
One of the important components of this approach is preparation of RE data set. Nsite uses the following 3 sets of human/animal and plant REs.
[1]: Set of human/animal REs prepared by merging and verification (excluding longer than 50 bp REs; elimination of redundancies) RE/TF information from ooTFD (Ghosh,D. Nucleic Acids Res, 2000, 28, 308- 310). It includes 8030 real/consensus REs.
[2]: Set of human/animal REs prepared by merging and verification RE/TF information from RegsiteAN DB developed Softberry Inc. It includes 1500 real/consensus REs.
[3]: Set of plant REs prepared by merging and verification RE/TF information from RegsitePL DB developed by Softberry Inc. The current version of this set includes 2359 real/consensus REs, but it is regularly updated.
Moreover, user can perform a search for motifs of REs from his own dataset in a format described below.
Input query sequences of length 100000 nucleotides or less must be given in FASTA format.
1. USER's set must include only sequences of real REs and/or their consensuses.
2. Every real RE/consensus is described in 3 lines:
LINE 1: Name/description of RE/consensus
LINE 2: Sequence of of RE/consensus
LINE 3: <par1> <par2> <par3> <par4>
3. Sequence (LINE2) may include both standard nucleotides (A/a, T/t, G/g,C/c)
and their any combinations in according to IUPAC abbreviations:R - A or G,
Y - T or C, K - G or T, M - A or C, S - G or C, W - A or T, B - G or T or C,
D - A or G or T, H - A or C or T, V - A or G or C, N - A or G or C or T.
In the case of composite REs, 2 boxes are seperated by "-".
Length of RE/consensus sequence must not exceed 80 symbols, including "-" in the case of composite elements.
Capital letters indicate Conservative nucleotides (positions) in which mismatch is not allowd.
4. In LINE 3:
<par1> - a maximal number of mismatches for the 1st box
<par2> - a maximal number of mismatches for the 2nd box (for composite REs)
If RE contains a single box, then <par2> = 0;
If any mismatch is not allowed, then <par1> = <par2> = 0 )
<par3> - minimal distance between boxes of composite RE
<par4> - maximal distance between boxes of composite RE (for a single-box REs <par3> = <par4> = 0 )
All <par1>, <par2>, <par3> and <par3> are given as INTEGER in 4i5 format.
RE 1 agTGGcgAggcg 2 0 0 0 RE2 caggccTGc-CCAGctgg 1 1 8 10 RE 3 RRTGTGGWWW 0 0 0 0
Every OUTPUT file begins with description of the Program's allocation, Search Parameters, as well as used abbreviations (in the case of using Data sets created by us). The next 2 includes name and length of the first query sequence. At last, name of REs, statistical estimation and sequences of motifs found are given.
For example: Program NsiteH | Version 5.2013 Search for motifs of 2356 RegulatoryElements (REs) in a pair of Homologous Sequences SET of REs: RegsitePDB: 2359 Plant Transcription REs [Last update: 05.02.2012; Softberry Inc] ____________________________________________________________ Search PARAMETRS: Expected Mean Number : 0.0500000 Statistical Siginicance Level : 0.9500000 Minimal Conservative Level : 80 % Level of homology between known RE and motif: 80% Variation of Distance between RE Blocks : 20% NOTE: RE - Regulatory Element/Consensus | AC - Accession No of RE in a given DB OS - Organism/Species | BF - Binding Factor or One of them Mism. - Mismatches | Mean. Exp. Number - Mean Expected Number | Up.Conf.Int. - Upper Confidence Interval ============================================================ QUERY: >gi|19674|emb|X12512.1| Nicotiana plumbaginifolia Cab-E gene 5'-flanking region Right Boundary of Upstream Sequence: 554 Length of Query Sequence: 554 bp | Nucleotide Frequencies: A - 0.34 G - 0.18 T - 0.31 C - 0.16 1 CATCCTTACT AACGGTAAAT AACTTAGAAG TTATTGTATA CGTATGATCG 51 AGCTGTTGGA CTTGTAGTAT CAAACTTTCA ATGACGCATC AAAATTAATT 101 ATGGTAGCTT CGCGTTGGGA CACTTGTACA TGCATTAACT TGATTTCAAT 151 TTCTTTTTTA AAAATATTTG TCTATTGTCA ATTTACCACT CGTACTTGAA 201 GTGGGCCTAT TTGACAGGTC AGCTAAATAC AGAAGTGTAT GAACAATGCG 251 TGGCCAAGAG TAACTCTTAT GCTAAAGACA AGTGGATATT ATATTGCAAT 301 AATCCACAAT CAGACGTGGC AAATTTGGAT TGGCTATAAG AGAGCAAATC 351 TTCATTAGGT AAGTTTTTTA AACATAAAAA GTATCTAAAA AAATCTTGTC 401 ATGTTTAACG GTGCTGAACT TTGCCAAATG GACAAGAATG CAAAAGGTTA 451 AAATTGCAAT CCACCAATTG AAAAGTAGAT ATAGATACTC AAGGATAAGG 501 GTCTTTGGGC CTGTAAAGCC ATTTATATAC ACTTAGTGCA AAGCCCATGA 551 AACT ............................................................ RE: 2. AC: RSP00002//OS: Brassica napus /GENE: Oleosin/RE: ABRE-3 /BF: B.napus embryo protein factor Motifs on "+" Strand: Mean Exp. Number 0.01834 Up.Conf.Int. 1 Found 1 -243 AgACGTGGC -235 (Mism.= 1; Cons.: 100 %) ............................................................ RE: 35. AC: RSP00035//OS: barley (Hordeum vulgare) /GENE: Al21/RE: D1 /BF: DOF Motifs on "+" Strand: Mean Exp. Number 0.04169 Up.Conf.Int. 1 Found 1 -114 CAAAAGG -108 (Mism.= 0; Cons.: 100 %) ............................................................ RE: 93. AC: RSP00093//OS: barley (Hordeum vulgare) /GENE: Amy pHV19/RE: TATCCAC box /BF: unknown nuclear factor Motifs on "-" Strand: Mean Exp. Number 0.03964 Up.Conf.Int. 1 Found 1 -267 TATCCAC -273 (Mism.= 0; Cons.: 85 %) ............................................................ RE: 204. AC: RSP00204//OS: arabidopsis (Arabidopsis thaliana) /GENE: AtEm6/RE: ABRE/6.2 /BF: ABI5 Motifs on "+" Strand: Mean Exp. Number 0.02794 Up.Conf.Int. 1 Found 1 -244 cAgACGTGGC -235 (Mism.= 2; Cons.: 100 %) ............................................................ RE: 208. AC: RSP00208//OS: French bean (Phaseolus vulgaris) /GENE: DLEC2/RE: DLEC2,A /BF: MAT2 (ROM2) Motifs on "-" Strand: Mean Exp. Number 0.00260 Up.Conf.Int. 1 Found 1 -235 GCCACGTCtGaT -246 (Mism.= 2; Cons.: 100 %) ............................................................ RE: 219. AC: RSP00219//OS: arabidopsis (Arabidopsis thaliana) /GENE: RBCS-1A/RE: G box-1 /BF: HY5; Arabidopsis bZIP protein - transcriptionl factor Motifs on "+" Strand: Mean Exp. Number 0.00908 Up.Conf.Int. 1 Found 1 -245 TcAgACGTGGCA -234 (Mism.= 2; Cons.: 100 %) ............................................................ RE: 248. AC: RSP00248//OS: rice (Oryza sativa), Oryza sativa /GENE: alpha-globulin/RE: REB2 /BF: REB Motifs on "-" Strand: Mean Exp. Number 0.00345 Up.Conf.Int. 1 Found 1 -235 GCCACGTCtG -244 (Mism.= 1; Cons.: 100 %) ............................................................ RE: 301. AC: RSP00301//OS: rice (Oryza sativa) (Oryza sativa) /GENE: GluB-1/RE: PROL box /BF: unknown nuclear factor Motifs on "+" Strand: Mean Exp. Number 0.03776 Up.Conf.Int. 1 Found 1 -18 TGCAAAG -12 (Mism.= 0; Cons.: 85 %) ............................................................ RE: 304. AC: RSP00304//OS: maize (Zea mays) /GENE: Synthetic oligonucleotides/RE: KN1/KIP BS /BF: KN1/KIP Motifs on "+" Strand: Mean Exp. Number 0.01171 Up.Conf.Int. 1 Found 1 -343 TGACAGGT -336 (Mism.= 0; Cons.: 87 %) ............................................................ RE: 629. AC: RSP00629//OS: arabidopsis (Arabidopsis thaliana) /GENE: Lhcb1*3/RE: CCA1 BS2 /BF: CCA1 Motifs on "+" Strand: Mean Exp. Number 0.04127 Up.Conf.Int. 1 Found 1 -166 AAAAATCT -159 (Mism.= 0; Cons.: 100 %) ............................................................ RE: 683. AC: RSP00683//OS: arabidopsis (Arabidopsis thaliana) /GENE: Adh/RE: -190 half G-box (core) /BF: GBF3 Motifs on "+" Strand: Mean Exp. Number 0.00753 Up.Conf.Int. 1 Found 1 -132 GCCAAaTGGA -123 (Mism.= 1; Cons.: 100 %) ............................................................ RE: 738. AC: RSP00738//OS: arabidopsis (Arabidopsis thaliana) /GENE: CAB2/RE: CUF-1 BS /BF: CUF-1 Motifs on "-" Strand: Mean Exp. Number 0.03677 Up.Conf.Int. 1 Found 1 -235 GCCACGTctG -244 (Mism.= 2; Cons.: 100 %) ................................................................................................... .................................................................................................... .................................................................................................... ............................................................ Totally 68 motifs of 66 different REs have been found Of them: 50 motifs of 49 different REs have Conservative Level >= 80 % ------------------------------------------------------------ QUERY: >gi|3036947|dbj|AB012638.1| Nicotiana sylvestris Lhcb1*5 genes for light harvesting chlorophyll a/b-binding protein, complete cds Right Boundary of Upstream Sequence: 520 Length of Query Sequence: 520 bp | Nucleotide Frequencies: A - 0.33 G - 0.18 T - 0.30 C - 0.18 1 ATCCCGAACC CAAAGTTTGA AATCCTGGCT CCGCCTCTGA TCCGTGCCCC 51 CTAAAGGCTT TTAGCATTAA GGGTGTCAAG TGATTTAAAT TAATCATTTT 101 CAAGGTATAC ACATATACAT ATACAAGATT TCTGCTGAAG TTTACGGGTC 151 CGCCACTGCA TACAAGTGGT CCTATTTTAC AGGTCAGCTA AATATACAGA 201 AGTGTATGAA CAATGCATGG CCAGGAGTTA CTCTTATGCT CTGGCTAAGT 251 TGATATTATA TTGCAATAAT CCACAATCAG ACGTGGCAAA TTTGGATTGG 301 CTATAAGAAG GAAATCTTCA TTGGCTTAGA TTTTTTAAAC GTATAAAGTA 351 TCTACAAAAA TCTAGTCATC TTTAACGGTG CAGAACTTTG CCAAATGGAA 401 AAGAATGCAA AAGGTTACAA ATTGTCATCC ACCAATGGAA AAGCAGATAT 451 AGATATTCAA GGATAAGGTA GTCTTTGGGC CTGTAAATTC ATTTATATAC 501 ACTTAGTACA AAGCCCATAA ............................................................ RE: 2. AC: RSP00002//OS: Brassica napus /GENE: Oleosin/RE: ABRE-3 /BF: B.napus embryo protein factor Motifs on "+" Strand: Mean Exp. Number 0.02276 Up.Conf.Int. 1 Found 1 -242 AgACGTGGC -234 (Mism.= 1; Cons.: 100 %) ............................................................ RE: 6. AC: RSP00006//OS: soybean (Glycine max) /GENE: GS15/RE: ATRE /BF: unknown nuclear factor Motifs on "+" Strand: Mean Exp. Number 0.02006 Up.Conf.Int. 1 Found 1 -36 AAATTcaTTTATAT -23 (Mism.= 2; Cons.: 85 %) ............................................................ RE: 35. AC: RSP00035//OS: barley (Hordeum vulgare) /GENE: Al21/RE: D1 /BF: DOF Motifs on "+" Strand: Mean Exp. Number 0.04055 Up.Conf.Int. 1 Found 1 -113 CAAAAGG -107 (Mism.= 0; Cons.: 100 %) ............................................................ RE: 204. AC: RSP00204//OS: arabidopsis (Arabidopsis thaliana) /GENE: AtEm6/RE: ABRE/6.2 /BF: ABI5 Motifs on "+" Strand: Mean Exp. Number 0.03270 Up.Conf.Int. 1 Found 1 -243 cAgACGTGGC -234 (Mism.= 2; Cons.: 100 %) ............................................................ RE: 208. AC: RSP00208//OS: French bean (Phaseolus vulgaris) /GENE: DLEC2/RE: DLEC2,A /BF: MAT2 (ROM2) Motifs on "-" Strand: Mean Exp. Number 0.00300 Up.Conf.Int. 1 Found 1 -234 GCCACGTCtGaT -245 (Mism.= 2; Cons.: 100 %) ............................................................ RE: 219. AC: RSP00219//OS: arabidopsis (Arabidopsis thaliana) /GENE: RBCS-1A/RE: G box-1 /BF: HY5; Arabidopsis bZIP protein - transcriptionl factor Motifs on "+" Strand: Mean Exp. Number 0.01014 Up.Conf.Int. 1 Found 1 -244 TcAgACGTGGCA -233 (Mism.= 2; Cons.: 100 %) ............................................................ RE: 248. AC: RSP00248//OS: rice (Oryza sativa), Oryza sativa /GENE: alpha-globulin/RE: REB2 /BF: REB Motifs on "-" Strand: Mean Exp. Number 0.00424 Up.Conf.Int. 1 Found 1 -234 GCCACGTCtG -243 (Mism.= 1; Cons.: 100 %) ............................................................ RE: 350. AC: RSP00350//OS: maize (Zea mays) /GENE: C1/RE: VP1 RE /BF: unknown nuclear factor Motifs on "-" Strand: Mean Exp. Number 0.04384 Up.Conf.Int. 1 Found 1 -298 tGgCCATGCAT -308 (Mism.= 2; Cons.: 90 %) ................................................................................ ................................................................................ ................................................................................ ............................................................ Totally 71 motifs of 67 different REs have been found Of them: 45 motifs of 44 different REs have Conservative Level >= 80 %