RANDTRAN: Random transcriptome sequence generator that accounts for partition specific features in eukaryotic mRNA datasets

Standard

RANDTRAN: Random transcriptome sequence generator that accounts for partition specific features in eukaryotic mRNA datasets. / Borzov, E.A.; Marakhonov, A.V.; Ivanov, M.V.; Drozdova, P.B.; Baranova, A.V.; Skoblov, M.Y.

в: Molecular Biology, № 5, 2014, стр. 749-756.

Результаты исследований: Научные публикации в периодических изданиях › статья › Рецензирование

Author

Borzov, E.A. ; Marakhonov, A.V. ; Ivanov, M.V. ; Drozdova, P.B. ; Baranova, A.V. ; Skoblov, M.Y. / RANDTRAN: Random transcriptome sequence generator that accounts for partition specific features in eukaryotic mRNA datasets. в: Molecular Biology. 2014 ; № 5. стр. 749-756.

BibTeX

@article{d57ebe7160e741dba885aa8f8005422d,

title = "RANDTRAN: Random transcriptome sequence generator that accounts for partition specific features in eukaryotic mRNA datasets",

abstract = "{\textcopyright} 2014, Pleiades Publishing, Inc. The generation of true random and pseudorandom control sequences is an important problem of computational biology. Available random sequence generators differ in underlying probabilistic models that often remain undisclosed to users. Random sequences produced by differing probabilistic models substantially differ in their outputs commonly used as baselines for evaluations of the motif frequencies. Moreover, modern bioinformatics studies often require generation of matching control transcriptome with emulated partitions into ORFs, 5- and 3-UTRs, as well as the proportion of non-coding RNAs within model transcriptome rather than relatively simple continuous control sequences. Here we describe novel random sequence generating tool RANDTRAN that accounts for the length distribution of 5′ and 3′ non-translated regions in given transcriptome and the partition-specific di- and trinucleotide compositions in translated and non-translated regions. RANDRAN presents matching control tran",

author = "E.A. Borzov and A.V. Marakhonov and M.V. Ivanov and P.B. Drozdova and A.V. Baranova and M.Y. Skoblov",

year = "2014",

doi = "10.1134/S0026893314050021",

language = "English",

pages = "749--756",

journal = "Molecular Biology",

issn = "0026-8933",

publisher = "Pleiades Publishing",

number = "5",

}

RIS

TY - JOUR

T1 - RANDTRAN: Random transcriptome sequence generator that accounts for partition specific features in eukaryotic mRNA datasets

AU - Borzov, E.A.

AU - Marakhonov, A.V.

AU - Ivanov, M.V.

AU - Drozdova, P.B.

AU - Baranova, A.V.

AU - Skoblov, M.Y.

PY - 2014

Y1 - 2014

N2 - © 2014, Pleiades Publishing, Inc. The generation of true random and pseudorandom control sequences is an important problem of computational biology. Available random sequence generators differ in underlying probabilistic models that often remain undisclosed to users. Random sequences produced by differing probabilistic models substantially differ in their outputs commonly used as baselines for evaluations of the motif frequencies. Moreover, modern bioinformatics studies often require generation of matching control transcriptome with emulated partitions into ORFs, 5- and 3-UTRs, as well as the proportion of non-coding RNAs within model transcriptome rather than relatively simple continuous control sequences. Here we describe novel random sequence generating tool RANDTRAN that accounts for the length distribution of 5′ and 3′ non-translated regions in given transcriptome and the partition-specific di- and trinucleotide compositions in translated and non-translated regions. RANDRAN presents matching control tran

AB - © 2014, Pleiades Publishing, Inc. The generation of true random and pseudorandom control sequences is an important problem of computational biology. Available random sequence generators differ in underlying probabilistic models that often remain undisclosed to users. Random sequences produced by differing probabilistic models substantially differ in their outputs commonly used as baselines for evaluations of the motif frequencies. Moreover, modern bioinformatics studies often require generation of matching control transcriptome with emulated partitions into ORFs, 5- and 3-UTRs, as well as the proportion of non-coding RNAs within model transcriptome rather than relatively simple continuous control sequences. Here we describe novel random sequence generating tool RANDTRAN that accounts for the length distribution of 5′ and 3′ non-translated regions in given transcriptome and the partition-specific di- and trinucleotide compositions in translated and non-translated regions. RANDRAN presents matching control tran

U2 - 10.1134/S0026893314050021

DO - 10.1134/S0026893314050021

M3 - Article

SP - 749

EP - 756

JO - Molecular Biology

JF - Molecular Biology

SN - 0026-8933

IS - 5

ER -

ID: 7061618