Tehdyt toimenpiteet
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banana |
Wiki
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Function
Plot bending and curvature data for B-DNADescription
banana predicts bending of a normal (B) DNA double helix, using the method of Goodsell & Dickerson, NAR 1994 11;22(24):5497-5503. The program calculates the magnitude of local bending and macroscopic curvature at each point along an arbitrary B-DNA sequence, using any desired bending model that specifies values of twist, roll and tilt as a function of sequence. The program outputs both a graphical display and a text file of the results.
The default model (model 'a' from the Goodsell & Dickerson paper) is based on the nucleosome positioning data of Satchwell et al 1986 (J. Mol. Biol. 191, 659-675). It correctly predicts experimental A-tract curvature as measured by gel retardation and cyclization kinetics and successfully predicts curvature in regions containing phased GGGCCC sequences. The model shows local bending at mixed sequence DNA, strong bends at the sequence GGC, and straight, rigid A-tracts. It is the only model out of the six investigated that is consistent with both solution data from gel retardation and cyclization kinetics and structural data from x-ray crystallography.
Algorithm
banana reads a sequence and a matrix of standard twist, roll and tilt angles for each type of base pair step. The default matrix is described below (see "Bending Model") but some other can be specified (see "Data Files" below). The program creates a table or a graphical image of the bending and the curvature at each base step.
The indicated twist, roll and tilt angles are applied at each step along the sequence, and the resulting base pair normal vector calculated. The first base pair is aligned normal to the z axis, with a twist value of 0.0 degrees. The specified twist is applied to the second base pair, and roll and tilt values are use to calculate its normal vector relative to the first. If either roll or tilt is non-zero, the new normal vector will be angled away from the z axis, producing the first 'bend'. The process is continued along the sequence, applying the appropriate twist, roll and tilt to each new base pair relative to its predecessor. The result is a list of normal vectors for all base pairs in the sequence.
Local bends are then calculated from the normal vectors. The bend for base N is calculated across a window from N-1 to N+1.
Curvature is calculated in two steps. Base pair normals are first averaged over a 10-base-pair window to filter out the local writhing of the helix. The normals of the nine base pairs from N-4 to N+4, and the two base pairs N-5 and N+5 at half weight, are averaged and assigned to base pair N. Curvature then is calculated from these averaged normal vector values, using a bracket value, nc, with a value of 15. That is, the curvature at base pair N is the angle between averaged normal vectors at base pairs N-nc and N+nc.
Bending Model
banana reads by default a data file (Eangles_tri.dat) of twist, roll and tilt angles, as in Goodsell & Dickerson, NAR 1994 11;22(24):5497-503 and Drew and Travers (1986) JMB 191, 659. The roll-tilt-twist parameters of this bending model are objective and unbiased. They are derived purely from experimental observations of sequence location preferences of base trimers in small circles of DNA, without reference to solution techniques that measure curvature per se.
Satchwell, Drew and Travers studied the positioning of DNA sequences wrappped around nucleosome cores, and in closed circles of double-helical DNA of comparable size. From the sequence data they calculated a fractional preference of each base pair triplet for a position 'facing out', or with the major groove on the concave side of the curved helix.
The sequence GGC, for example, has a 45% preference for locations on a bent double helix in which its major groove faces inward and is compressed by the curvature (tending towards positive roll), whereas sequence AAA has a 36% preference for the opposite orientation, with major groove facing outward and with minor groove facing inward and compressed (tending toward negative roll).
These fractional variances are converted into roll angles in the following manner: Because x-ray cyrstal structure analysis uniformly indicates that AA steps are unbent, a zero roll is assigned to the AAA triplet; an arbitrary maximum roll of 10 degrees is asigned to GGC, and all other triplets are scaled in a lenear manner. Where % is the percent-out figure, then: Roll = 10 degrees * (% + 36)/(45 + 36)
Changing the maximum roll value will scale the entire profile up or down proportionately, but will not change the shape of the profile. Peaks will remain peaks, and valleys, valleys. The absolute magnitude of all the roll values is less important than their relative magnitude, or the order of roll preference. Twist angles were set to zero. Because these values correspond to base trimers, the values of roll, tilt and twist were applied to the first two bases for the calculation.
Usage
Here is a sample session with banana
% banana -nooutfile -graph ps Plot bending and curvature data for B-DNA Input nucleotide sequence: tembl:u68037 Created banana.ps |
Go to the input files for this example
Go to the output files for this example
Example 2
% banana -graph data Plot bending and curvature data for B-DNA Input nucleotide sequence: tembl:u68037 Created banana1.dat Created banana2.dat Created banana3.dat Created banana4.dat Created banana5.dat Created banana6.dat Created banana7.dat Created banana8.dat Created banana9.dat |
Go to the output files for this example
Command line arguments
Plot bending and curvature data for B-DNA
Version: EMBOSS:6.4.0.0
Standard (Mandatory) qualifiers:
[-sequence] sequence Nucleotide sequence filename and optional
format, or reference (input USA)
-graph graph [$EMBOSS_GRAPHICS value, or x11] Graph type
(ps, hpgl, hp7470, hp7580, meta, cps, x11,
tek, tekt, none, data, xterm, png, gif, pdf,
svg)
Additional (Optional) qualifiers:
-anglesfile datafile [Eangles_tri.dat] DNA base trimer roll
angles data file
-residuesperline integer [50] Number of residues to be displayed on
each line (Any integer value)
-outfile outfile [banana.profile] Output file name
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-sequence" associated qualifiers
-sbegin1 integer Start of the sequence to be used
-send1 integer End of the sequence to be used
-sreverse1 boolean Reverse (if DNA)
-sask1 boolean Ask for begin/end/reverse
-snucleotide1 boolean Sequence is nucleotide
-sprotein1 boolean Sequence is protein
-slower1 boolean Make lower case
-supper1 boolean Make upper case
-sformat1 string Input sequence format
-sdbname1 string Database name
-sid1 string Entryname
-ufo1 string UFO features
-fformat1 string Features format
-fopenfile1 string Features file name
"-graph" associated qualifiers
-gprompt boolean Graph prompting
-gdesc string Graph description
-gtitle string Graph title
-gsubtitle string Graph subtitle
-gxtitle string Graph x axis title
-gytitle string Graph y axis title
-goutfile string Output file for non interactive displays
-gdirectory string Output directory
"-outfile" associated qualifiers
-odirectory string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options and exit. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
-version boolean Report version number and exit
|
| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-sequence] (Parameter 1) |
sequence | Nucleotide sequence filename and optional format, or reference (input USA) | Readable sequence | Required |
| -graph | graph | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, pdf, svg | EMBOSS_GRAPHICS value, or x11 |
| Additional (Optional) qualifiers | ||||
| -anglesfile | datafile | DNA base trimer roll angles data file | Data file | Eangles_tri.dat |
| -residuesperline | integer | Number of residues to be displayed on each line | Any integer value | 50 |
| -outfile | outfile | Output file name | Output file | banana.profile |
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-sequence" associated sequence qualifiers | ||||
| -sbegin1 -sbegin_sequence |
integer | Start of the sequence to be used | Any integer value | 0 |
| -send1 -send_sequence |
integer | End of the 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 | |
| "-graph" associated graph qualifiers | ||||
| -gprompt | boolean | Graph prompting | Boolean value Yes/No | N |
| -gdesc | string | Graph description | Any string | Bending and curvature plot |
| -gtitle | string | Graph title | Any string | |
| -gsubtitle | string | Graph subtitle | Any string | |
| -gxtitle | string | Graph x axis title | Any string | |
| -gytitle | string | Graph y axis title | Any string | |
| -goutfile | string | Output file for non interactive displays | Any string | |
| -gdirectory | string | Output directory | Any string | |
| "-outfile" associated outfile qualifiers | ||||
| -odirectory | 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 |
Input file format
banana reads a single nucleotide sequences.
The output is a standard EMBOSS sequence file.
The results can be output in one of several styles by using the command-line qualifier -osformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq, excel, feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq.
See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.
Input files for usage example
'tembl:u68037' is a sequence entry in the example nucleic acid database 'tembl'
Database entry: tembl:u68037
ID U68037; SV 1; linear; mRNA; STD; ROD; 1218 BP.
XX
AC U68037;
XX
DT 23-SEP-1996 (Rel. 49, Created)
DT 04-MAR-2000 (Rel. 63, Last updated, Version 2)
XX
DE Rattus norvegicus EP1 prostanoid receptor mRNA, complete cds.
XX
KW .
XX
OS Rattus norvegicus (Norway rat)
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea;
OC Muridae; Murinae; Rattus.
XX
RN [1]
RP 1-1218
RA Abramovitz M., Boie Y.;
RT "Cloning of the rat EP1 prostanoid receptor";
RL Unpublished.
XX
RN [2]
RP 1-1218
RA Abramovitz M., Boie Y.;
RT ;
RL Submitted (26-AUG-1996) to the EMBL/GenBank/DDBJ databases.
RL Biochemistry & Molecular Biology, Merck Frosst Center for Therapeutic
RL Research, P. O. Box 1005, Pointe Claire - Dorval, Quebec H9R 4P8, Canada
XX
DR Ensembl-GO; ENSRNOESTG00000830631; Rattus_norvegicus.
DR Ensembl-Gn; ENSRNOG00000004094; Rattus_norvegicus.
DR Ensembl-Gn; ENSRNOG00000017743; Rattus_norvegicus.
DR Ensembl-TO; ENSRNOESTT00000830623; Rattus_norvegicus.
DR Ensembl-Tr; ENSRNOT00000005470; Rattus_norvegicus.
DR Ensembl-Tr; ENSRNOT00000023860; Rattus_norvegicus.
XX
FH Key Location/Qualifiers
FH
FT source 1..1218
FT /organism="Rattus norvegicus"
FT /strain="Sprague-Dawley"
FT /mol_type="mRNA"
FT /db_xref="taxon:10116"
FT CDS 1..1218
FT /codon_start=1
FT /product="EP1 prostanoid receptor"
FT /note="family 1 G-protein coupled receptor"
FT /db_xref="GOA:P70597"
FT /db_xref="InterPro:IPR000276"
FT /db_xref="InterPro:IPR000708"
FT /db_xref="InterPro:IPR001244"
FT /db_xref="InterPro:IPR008365"
FT /db_xref="InterPro:IPR017452"
FT /db_xref="UniProtKB/Swiss-Prot:P70597"
FT /protein_id="AAB07735.1"
FT /translation="MSPYGLNLSLVDEATTCVTPRVPNTSVVLPTGGNGTSPALPIFSM
FT TLGAVSNVLALALLAQVAGRLRRRRSTATFLLFVASLLAIDLAGHVIPGALVLRLYTAG
FT RAPAGGACHFLGGCMVFFGLCPLLLGCGMAVERCVGVTQPLIHAARVSVARARLALALL
FT AAMALAVALLPLVHVGHYELQYPGTWCFISLGPPGGWRQALLAGLFAGLGLAALLAALV
FT CNTLSGLALLRARWRRRRSRRFRENAGPDDRRRWGSRGLRLASASSASSITSTTAALRS
FT SRGGGSARRVHAHDVEMVGQLVGIMVVSCICWSPLLVLVVLAIGGWNSNSLQRPLFLAV
FT RLASWNQILDPWVYILLRQAMLRQLLRLLPLRVSAKGGPTELSLTKSAWEASSLRSSRH
FT SGFSHL"
XX
SQ Sequence 1218 BP; 162 A; 397 C; 387 G; 272 T; 0 other;
atgagcccct acgggcttaa cctgagccta gtggatgagg caacaacgtg tgtaacaccc 60
agggtcccca atacatctgt ggtgctgcca acaggcggta acggcacatc accagcgctg 120
cctatcttct ccatgacgct gggtgctgtg tccaacgtgc tggcgctggc gctgctggcc 180
caggttgcag gcagactgcg gcgccgccgc tcgactgcca ccttcctgtt gttcgtcgcc 240
agcctgcttg ccatcgacct agcaggccat gtgatcccgg gcgccttggt gcttcgcctg 300
tatactgcag gacgtgcgcc cgctggcggg gcctgtcatt tcctgggcgg ctgtatggtc 360
ttctttggcc tgtgcccact tttgcttggc tgtggcatgg ccgtggagcg ctgcgtgggt 420
gtcacgcagc cgctgatcca cgcggcgcgc gtgtccgtag cccgcgcacg cctggcacta 480
gccctgctgg ccgccatggc tttggcagtg gcgctgctgc cactagtgca cgtgggtcac 540
tacgagctac agtaccctgg cacttggtgt ttcattagcc ttgggcctcc tggaggttgg 600
cgccaggcgt tgcttgcggg cctcttcgcc ggccttggcc tggctgcgct ccttgccgca 660
ctagtgtgta atacgctcag cggcctggcg ctccttcgtg cccgctggag gcggcgtcgc 720
tctcgacgtt tccgagagaa cgcaggtccc gatgatcgcc ggcgctgggg gtcccgtgga 780
ctccgcttgg cctccgcctc gtctgcgtca tccatcactt caaccacagc tgccctccgc 840
agctctcggg gaggcggctc cgcgcgcagg gttcacgcac acgacgtgga aatggtgggc 900
cagctcgtgg gcatcatggt ggtgtcgtgc atctgctgga gccccctgct ggtattggtg 960
gtgttggcca tcgggggctg gaactctaac tccctgcagc ggccgctctt tctggctgta 1020
cgcctcgcgt cgtggaacca gatcctggac ccatgggtgt acatcctgct gcgccaggct 1080
atgctgcgcc aacttcttcg cctcctaccc ctgagggtta gtgccaaggg tggtccaacg 1140
gagctgagcc taaccaagag tgcctgggag gccagttcac tgcgtagctc ccggcacagt 1200
ggcttcagcc acttgtga 1218
//
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Output file format
The output is to both a graphical display and to a text file with the default name 'banana.profile'.The graphical display shows the sequence together with the local local bending (solid line) and macroscopic curvature (dotted line).
The output is to the specified graphics device.
The results can be output in one of several formats by using the command-line qualifier -graph xxx, where 'xxx' is replaced by the name of the required device. Support depends on the availability of third-party software packages.
The device names that output to a file are: ps (postscript), cps (colourps), png, gif, pdf, svg, hpgl, hp7470, hp7580, das, data.
The other available device names are: meta, x11 (xwindows), tek (tek4107t), tekt (tektronix), xterm, text.
Output can be turned off by specifying none (null).
See: http://emboss.sf.net/docs/themes/GraphicsDevices.html for further information on supported devices.
Output files for usage example
Graphics File: banana.ps
![[banana results]](banana.1.banana.gif)
Output files for usage example 2
File: banana.profile
Base Bend Curve a 0.0 0.0 t 19.7 0.0 g 17.7 0.0 a 21.1 0.0 g 28.5 0.0 c 26.2 0.0 c 19.7 0.0 c 18.7 0.0 c 12.5 0.0 t 9.7 0.0 a 14.9 0.0 c 16.5 0.0 g 17.5 0.0 g 26.2 0.0 g 28.5 0.0 c 20.7 0.0 t 11.7 0.0 t 6.4 0.0 a 9.3 0.0 a 14.9 0.0 c 17.7 20.0 c 15.7 19.2 t 15.7 18.5 g 17.7 17.9 a 21.1 17.1 g 28.5 15.9 c 25.2 14.6 c 12.5 13.3 t 7.2 11.9 a 13.2 10.8 g 20.1 10.1 t 19.5 9.6 g 15.1 9.2 g 14.9 9.1 a 19.5 9.5 t 19.7 10.2 g 17.7 10.8 a 17.7 11.0 g 25.2 11.2 g 26.2 11.3 c 15.3 11.5 a 11.4 11.7 a 14.5 12.0 c 13.9 12.2 a 11.4 12.3 a 14.9 12.5 c 17.7 12.8 g 19.5 13.3 t 19.1 13.5 [Part of this file has been deleted for brevity] g 15.1 15.2 a 17.7 15.5 g 25.2 15.8 g 32.5 16.0 c 25.2 15.8 c 15.7 15.0 a 16.3 14.2 g 15.5 13.5 t 10.8 12.8 t 13.7 12.3 c 19.5 12.1 a 20.1 12.1 c 16.3 12.1 t 16.7 11.9 g 22.1 11.4 c 21.1 11.1 g 14.9 10.7 t 9.7 10.3 a 16.1 9.8 g 24.5 9.4 c 21.1 8.9 t 15.1 8.4 c 16.1 7.7 c 17.5 7.3 c 15.3 6.9 g 24.0 6.4 g 26.2 5.8 c 20.5 5.4 a 19.1 5.1 c 15.3 26.0 a 16.3 0.0 g 20.1 0.0 t 19.5 0.0 g 25.2 0.0 g 28.5 0.0 c 20.7 0.0 t 13.3 0.0 t 13.7 0.0 c 15.7 0.0 a 19.1 0.0 g 28.5 0.0 c 25.2 0.0 c 19.5 0.0 a 20.1 0.0 c 17.9 0.0 t 13.9 0.0 t 13.9 0.0 g 19.1 0.0 t 19.5 0.0 g 0.0 0.0 a 0.0 0.0 |
File: banana1.dat
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File: banana5.dat
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File: banana6.dat
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The data file consists of three columns separated by blanks or tab characters.
The first column is the sequence.
The second column is the local bending.
The third is the curvature.
Data files
banana requires a data file in the EMBOSS data directory containing the twist, roll and tilt angles. By default Eangles_tri.dat is used, as in Goodsell & Dickerson, NAR 1994 11;22(24):5497-503 and Drew and Travers (1986) JMB 191, 659. Some other file may be specified with the -anglesfile option.The description of this bending model is as follows:
The roll-tilt-twist parameters of this model are derived purely from experimental observations of sequence location preferences of base trimers in small circles of DNA, without reference to solution techniques that measure curvature per se. For this reason, they may be the most objective and unbiased parameters of all. Satchwell, Drew and Travers studied the positioning of DNA sequences wrappped around nucleosome cores, and in closed circles of double-helical DNA of comparable size. From the sequence data they calculated a fractional preference of each base pair triplet for a position 'facing out', or with the major groove on the concave side of the curved helix. The sequence GGC, for example, has a 45% preference for locations on a bent double helix in which its major groove faces inward and is compressed by the curvature (tending towards positive roll), whereas sequence AAA has a 36% preference for the opposite orientation, with major groove facing outward and with minor groove facing inward and compressed (tending toward negative roll). These fractional variances have been converted into roll angles in the following manner: Because x-ray cyrstal structure analysis uniformly indicates that AA steps are unbent, a zero roll is assigned to the AAA triplet; an arbitrary maximum roll of 10 degrees is asigned to GGC, and all other triplets are scaled in a lenear manner. Where % is the percent-out figure, then:
Roll = 10 degrees * (% + 36)/(45 + 36)
Changing the maximum roll value will scale the entire profile up or down proportionately, but will not change the shape of the profile. Peaks will remain peaks, and valleys, valleys. The absolute magnitide of all the roll values is less important than their relative magnitude, or the order of roll preference. Twist angles were set to zero. Because these values correspond to base trimers, the values of roll, tilt and twist were applied to the first two bases for the calculation.
Notes
DNA bending is vital for the winding of DNA in nucleosomes, and the recognition of particular DNA loci by restriction enzymes, repressors and other control proteins. For example, the binding of the catabolite gene activator protein and of the TATA-box recognition protein to a double DNA helix both rely on major bends in the helix induced at specific sequence loci. Whether the particular recognition sequences are bent even in the absence of proteins is not always clear: a preformed bend in the DNA would form a custom site for protein binding, or an enhanced bendability of a given sequence would facilitate protein-induced bending. Sadly, the rules of sequence-dependent DNA bending remain elusive.
Two models of sequence-dependent bending in free DNA have been proposed. Nearest neighbor models propose that large-scale measurable curvature may arise by the accumulation of many small local deformations in helical twist, roll, tilt and slide at individual steps between base pairs. In contrast, junction models propose that bending occurs at the interface between two different structural variants of the B-DNA double helix.
In both models, sequences which are anisotropically bendable - for instance, sequences with steps that preferentially bend only to compress the major groove - will lead to an average structure which is similar to a sequence with a rigid, intrinsic bend. The default bending model (see below) used by banana does not distinguish between these two possibilities.
B-DNA has the special property of having its base pairs very nearly perpendicular to the overall helix axis. Hence the normal vector to each base pair can be taken as representing the local helix at that point, and curvature and bending can be studied simply by observing the behaviour of the normal vectors from one base to another along the helix. This is both easy to calculate and simple to interpret. This program display the magnitude of bending and curvature at each point along the sequence. It is not intended as a substitute for more elaborate three-dimensional trajectory calculations, but only to express bending tendencies as a function of sequence. This affords easy screening for regions of a given DNA sequence where phased local bends add constructively to form an overall curve.
The terms bending and curvature are used in a restricted sense here. Bending of DNA describes the tendency for successive base pairs to be non-parallel in an additive manner over several base pair steps. Bending most commonly is produced by a rolling of adjacent base pairs over one another about thir long axis, although in principle, tilting of base pairs about their short axis could make a contribution. In contrast curvature of DNA represents the tendency of the helix axis to follow a non-linear pathway over an appreciable length, in a manner that contributes to macroscopic behaviour such as gel retardation or ease of cyclization into DNA minicircles.
The distinction between local bending and macroscopic curvature is illustrated (poorly) in the following figure (see figure 1 of the Goodsell & Dickerson paper for a better view).
bend bend bend
- - -
uncurved / \ / \ / \
-----/ \-/ \-/ \-----
bend bend
bend bend
/-------\
/ \
curved |bend |bend
| |
| |
X-ray crystal structure analysis cannot show curvature, but can and often does show local bending. Conversely, gel electrophoresis and cyclization kinetics can detect macroscopic curvature, but not bending. A complete knowledge of local bending would permit the precise calculation of curvature, but a knowledge of macroscopic curvature alone does not allow one to specify precisely the local bending elements that produce it. This paradox has plagued the DNA conformation field resembles the familiar problem of classical statistical mechanics, where a complete knowledge of positions and velocities of all molecules of a gas would allow one to calculate bulk properties such as temperature, pressure and volume, but knowledge of bulk properties cannot lead one to precise molecular positions. Many molecular arrangements can produce identical bulk properties, and in the present case, many bending combinations can produce identical macroscopic curvature.
The consensus sequence for DNA bending is 5 As and 5 non-As alternating. "N" is an ambiguity code for any base, and "B" is the ambiguity code for "not A" so "BANANA" is itself a bent sequence - hence the name of this program.
References
- Goodsell, D.S. & Dickerson, R.E. (1994) "Bending and Curvature Calculations in B-DNA" Nucl. Acids. Res. 22, 5497-5503.
- Drew and Travers (1986) JMB 191, 659
Warnings
Only ACTG allowed, if sequence contains a non ACTG character then the program will exit with a fatal error message.Diagnostic Error Messages
None.Exit status
0 if successful.Known bugs
None.See also
| Program name | Description |
|---|---|
| btwisted | Calculate the twisting in a B-DNA sequence |
| chaos | Draw a chaos game representation plot for a nucleotide sequence |
| compseq | Calculate the composition of unique words in sequences |
| dan | Calculates nucleic acid melting temperature |
| density | Draw a nucleic acid density plot |
| einverted | Finds inverted repeats in nucleotide sequences |
| freak | Generate residue/base frequency table or plot |
| isochore | Plots isochores in DNA sequences |
| sirna | Finds siRNA duplexes in mRNA |
| wordcount | Count and extract unique words in molecular sequence(s) |
Author(s)
Ian Longden formerly at:Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.