• Something wrong with this record ?

Palindrome analyser - A new web-based server for predicting and evaluating inverted repeats in nucleotide sequences

V. Brázda, J. Kolomazník, J. Lýsek, L. Hároníková, J. Coufal, J. Št'astný,

. 2016 ; 478 (4) : 1739-45. [pub] 20160904

Language English Country United States

Document type Journal Article

Persistent link   https://www.medvik.cz/link/bmc17023720

DNA cruciform structures play an important role in the regulation of natural processes including gene replication and expression, as well as nucleosome structure and recombination. They have also been implicated in the evolution and development of diseases such as cancer and neurodegenerative disorders. Cruciform structures are formed by inverted repeats, and their stability is enhanced by DNA supercoiling and protein binding. They have received broad attention because of their important roles in biology. Computational approaches to study inverted repeats have allowed detailed analysis of genomes. However, currently there are no easily accessible and user-friendly tools that can analyse inverted repeats, especially among long nucleotide sequences. We have developed a web-based server, Palindrome analyser, which is a user-friendly application for analysing inverted repeats in various DNA (or RNA) sequences including genome sequences and oligonucleotides. It allows users to search and retrieve desired gene/nucleotide sequence entries from the NCBI databases, and provides data on length, sequence, locations and energy required for cruciform formation. Palindrome analyser also features an interactive graphical data representation of the distribution of the inverted repeats, with options for sorting according to the length of inverted repeat, length of loop, and number of mismatches. Palindrome analyser can be accessed at http://bioinformatics.ibp.cz.

References provided by Crossref.org

000      
00000naa a2200000 a 4500
001      
bmc17023720
003      
CZ-PrNML
005      
20170720122325.0
007      
ta
008      
170720s2016 xxu f 000 0|eng||
009      
AR
024    7_
$a 10.1016/j.bbrc.2016.09.015 $2 doi
035    __
$a (PubMed)27603574
040    __
$a ABA008 $b cze $d ABA008 $e AACR2
041    0_
$a eng
044    __
$a xxu
100    1_
$a Brázda, Václav $u Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic. Electronic address: vaclav@ibp.cz.
245    10
$a Palindrome analyser - A new web-based server for predicting and evaluating inverted repeats in nucleotide sequences / $c V. Brázda, J. Kolomazník, J. Lýsek, L. Hároníková, J. Coufal, J. Št'astný,
520    9_
$a DNA cruciform structures play an important role in the regulation of natural processes including gene replication and expression, as well as nucleosome structure and recombination. They have also been implicated in the evolution and development of diseases such as cancer and neurodegenerative disorders. Cruciform structures are formed by inverted repeats, and their stability is enhanced by DNA supercoiling and protein binding. They have received broad attention because of their important roles in biology. Computational approaches to study inverted repeats have allowed detailed analysis of genomes. However, currently there are no easily accessible and user-friendly tools that can analyse inverted repeats, especially among long nucleotide sequences. We have developed a web-based server, Palindrome analyser, which is a user-friendly application for analysing inverted repeats in various DNA (or RNA) sequences including genome sequences and oligonucleotides. It allows users to search and retrieve desired gene/nucleotide sequence entries from the NCBI databases, and provides data on length, sequence, locations and energy required for cruciform formation. Palindrome analyser also features an interactive graphical data representation of the distribution of the inverted repeats, with options for sorting according to the length of inverted repeat, length of loop, and number of mismatches. Palindrome analyser can be accessed at http://bioinformatics.ibp.cz.
650    _2
$a sekvence nukleotidů $7 D001483
650    _2
$a výpočetní biologie $x metody $7 D019295
650    _2
$a DNA $x analýza $x genetika $7 D004247
650    _2
$a DNA bakterií $x analýza $x genetika $7 D004269
650    _2
$a křížová struktura DNA $x analýza $x genetika $7 D045566
650    _2
$a DNA virů $x analýza $x genetika $7 D004279
650    _2
$a Escherichia coli $x genetika $7 D004926
650    _2
$a genom bakteriální $x genetika $7 D016680
650    _2
$a genom virový $x genetika $7 D016679
650    12
$a internet $7 D020407
650    _2
$a obrácené repetice $x genetika $7 D055029
650    _2
$a oligonukleotidy $x analýza $x genetika $7 D009841
650    _2
$a reprodukovatelnost výsledků $7 D015203
650    _2
$a viry $x klasifikace $x genetika $7 D014780
655    _2
$a časopisecké články $7 D016428
700    1_
$a Kolomazník, Jan $u Mendel University in Brno, Zemědělská 1, 613 00, Brno, Czech Republic.
700    1_
$a Lýsek, Jiří $u Mendel University in Brno, Zemědělská 1, 613 00, Brno, Czech Republic.
700    1_
$a Hároníková, Lucia $u Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic.
700    1_
$a Coufal, Jan $u Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic.
700    1_
$a Št'astný, Jiří $u Mendel University in Brno, Zemědělská 1, 613 00, Brno, Czech Republic.
773    0_
$w MED00009307 $t Biochemical and biophysical research communications $x 1090-2104 $g Roč. 478, č. 4 (2016), s. 1739-45
856    41
$u https://pubmed.ncbi.nlm.nih.gov/27603574 $y Pubmed
910    __
$a ABA008 $b sig $c sign $y a $z 0
990    __
$a 20170720 $b ABA008
991    __
$a 20170720122818 $b ABA008
999    __
$a ok $b bmc $g 1239401 $s 984633
BAS    __
$a 3
BAS    __
$a PreBMC
BMC    __
$a 2016 $b 478 $c 4 $d 1739-45 $e 20160904 $i 1090-2104 $m Biochemical and biophysical research communications $n Biochem Biophys Res Commun $x MED00009307
LZP    __
$a Pubmed-20170720

Find record

Citation metrics

Archiving options