A Linear Algorithm for the Dete tion of Evolutive Tandem Repeats

نویسنده

  • Martine Léonard
چکیده

Abstra t. We present here a linear algorithm for the dete tion of evolutive tandem repeats. An evolutive tandem repeat onsists in a series of almost ontiguous opies, every opy being similar (using Hamming distan e in this arti le) to its prede essor and su essor. From a global view point, evolutive tandem repeats extend the traditional approximate tandem repeat where ea h opy has to be in a neighborhood of a given model. Due to the la k of algorithms, these repeats have been dis overed in genomi sequen es only re ently. In this arti le, we present a two-stage algorithm, where we rst ompute an array ontaining all the Hamming distan es between andidates, then we visit this array to build a omplete evolutive tandem repeat from insulated pairs of opies. Moreover, we explain how it is still onsistent with the usual te hnique devoted to dynami programming whi h onsists in lling a omparison matrix and ba ktra king through it to nd an optimal alignment.

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

A Linear Algorithm for the Detection of Evolutive Tandem Repeats

Abstra t. We present here a linear algorithm for the dete tion of evolutive tandem repeats. An evolutive tandem repeat onsists in a series of almost ontiguous opies, every opy being similar (using Hamming distan e in this arti le) to its prede essor and su essor. From a global view point, evolutive tandem repeats extend the traditional approximate tandem repeat where ea h opy has to be in a nei...

متن کامل

Speeding up the detection of evolutive tandem repeats

We recently introduced evolutive tandem repeats with jump (using Hamming distance) (Proc. MFCS’02: the 27th Internat. Symp. Mathematical Foundations of Computer Science, Warszawa, Otwock, Poland, August 2002, Lecture Notes in Computer Science, Vol. 2420, Springer, Berlin, pp. 292–304) which consist in a series of almost contiguous copies having the following property: the Hamming distance betwe...

متن کامل

A Distribution Detection Framework for Watermark Analysis

ABSTRACT Many watermarking algorithms have been proposed and studied for their robustness and other properties. But, there has been little e ort is analyzing these algorithms for their vulnerability against dete tion by an adversary. As a general philosophy for robust watermarking the host signal and the watermarked signal are well separated in a statisti al distan e sense. This very nature an ...

متن کامل

A Threshold Accepting Algorithm for Partitioning Machines in a Tandem Automated Guided Vehicle

Abstract : A tandem automated guided vehicle (AGV) system deals with grouping workstations into some non-overlapping zones , and assigning exactly one AGV to each zone. This paper presents a new non-linear integer mathematical model to group n machines into N loops that minimizes both inter and intra-loop flows simultaneously. Due to computational difficulties of exact methods in solving our pr...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

عنوان ژورنال:

دوره   شماره 

صفحات  -

تاریخ انتشار 2016