Repeat finding tools

Repeat a Word Five Times. This example repeats the word "meow" 5 times and separate it by the space character. Required options These options will be used automatically if you select this example. Number Number of repetitions. Delimiter Delimiter for output copies. Repeat a Column. In this example, we set a newline character in the separator field and as a result, we got a column with 20 repetitions of the phrase "Wake up! Wake up! Decimal Repetitions. This example uses a fractional number 3.

The number 3. Pro tips Master online text tools. You can pass input to this tool via? Here's how to type it in your browser's address bar. Click to try! All text tools. Didn't find the tool you were looking for? Let us know what tool we are missing and we'll build it! Split Text.

Quickly split text into chunks. Join Text. Quickly merge lines of text together via a delimiter. Repeat Text. Quickly repeat text many times. Reverse Text. Quickly write text backwards. Truncate Text. Quickly cut text to the given length. Trim Text.

Quickly trim left or right side of text. Left-pad Text. Quickly pad the left side of text. Right-pad Text. Quickly pad the right side of text. Right-align Text. Quickly align text to the right side. Center Text. Add a Prefix to Text. Quickly prepend a prefix to text. Add a Suffix to Text. Quickly append a suffix to text. Remove All Empty Lines. Quickly delete all blank lines from text.

Remove All Duplicate Lines. Quickly delete all repeated lines from text. Filter Text Lines. Quickly return text lines that match a string or a regex. Extract a Text Fragment. Quickly extract a text snippet of the given length. Find and Replace Text. Quickly find and replace text patterns. Find the Length of Text. Quickly count the number of characters in text. Count Text Lines. Quickly find the number of lines in text. Add Line Numbers.

Quickly add a number before every text line. Create an Image from Text. Quickly create an image from text. Generate Zalgo Text. Apply the Zalgo effect to the input text. Create a Palindrome. Quickly construct a palindrome from plain text. Check if Text is a Palindrome. Quickly test if text is a palindrome. Change Text Case. Quickly switch between various letter cases in text.

Convert Text to Uppercase. Quickly convert text letters to uppercase. Convert Text to Lowercase. Quickly convert text letters to lowercase. Randomize Text Case. Quickly randomize character case in text. Invert Text Case. Quickly invert character case in text. Convert Spaces to Newlines. Quickly replace spaces with newlines in text. Convert Newlines to Spaces.

Quickly replace newlines with spaces in text. Convert Spaces to Tabs. Quickly get tabs instead of spaces in text. Convert Tabs to Spaces. Quickly get spaces instead of tabs in text. Remove All Whitespace. Quickly clear text from spaces, tabs, and newlines. Remove All Punctuation. Quickly clear text from dots, commas, and similar characters. Quickly extract tag content from HTML code. Extract Text from XML.

Quickly extract tag content from an XML document. Extract Text from BBCode. Quickly extract all textual data from BBCode markup. Clicking on the location indices for one of the table entries opens a second web browser that shows an alignment of the copies against a consensus pattern.

The program is very fast, analyzing sequences on the order of. Submitted sequences may be of arbitrary length. This tells us that both in each genotype and in general, each repeat occurs the same number of times.

The validation method we chose to use for RepeatAnalyzer, though it allowed us to test our identification functionality in a large set of test cases, relies on the assumption that GenBank data is correct. In particular, if a DNA sequence is reported correctly in a paper and uploaded incorrectly to GenBank, our validation method would mark that as an error. This can be viewed as a limitation. However, due to the rarity of a mismatch between GenBank and the literature we chose to trust the veracity of GenBank data.

When compiling A. We found some papers [ 33 , 45 ] that opted against naming strains at all, perhaps due to the uncertainty faced on how best to name strains. A naming scheme containing the location of the strain and the genotype was proposed by Cabezas-Cruz [ 32 ].

However, while an improvement, this nomenclature system leaves out year, which nonetheless might be an important piece of information in the future, for example, to determine whether the same genotype is occurring year after year in a particular region.

Adding animal id allows someone to quickly realize that in the Kansas study the 6 D E genotype occurred seven times. In summary, we have developed a new software tool for storing, managing, identifying and analysing short-sequence repeats for the purpose of strain identification. Our software can take a gene sequence and return the repeats it contains along with the known strain if any that the sequence belongs to.

It does so by storing data distilled from sources on repeats at a given SSR locus. The data can be updated simply and searched easily for information about any known strains or repeats. All of these tasks are done in a computationally efficient manner using the KMP string matching algorithm and general programming best practices. RepeatAnalyzer can also produce a map for any combination of repeats and strains in a given region, offering geographic insights into their distribution not previously available.

In addition, it can calculate metrics of diversity within geographic regions. We intend to maintain a periodically updated version of the A. Short-sequence DNA repeats in prokaryotic genomes. Microbiol Mol Biol Rev.

DNA repeats identify novel virulence genes in Haemophilus influenzae. Molecular typing of Staphylococcus aureus on the basis of coagulase gene polymorphisms. J Clin Microbiol. Diversity of PspA: mosaic genes and evidence for past recombination in Streptococcus pneumoniae. Infect Immun. Yother J, Briles DE. Structural properties and evolutionary relationships of PspA, a surface protein of Streptococcus pneumoniae , as revealed by sequence analysis.

J Bacteriol. Molecular basis for surface antigen size polymorphisms and conservation of a neutralization-sensitive epitope in Anaplasma marginale. Proc Natl Acad Sci. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. Searching for patterns in genomic data.

Trends Genet. Farre D. BMC Bioinformatics. Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob DNA. Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor.

RepeatMasker Open Accessed 8 Oct PSSRdb: a relational database of polymorphic simple sequence repeats extracted from prokaryotic genomes. REPuter: the manifold applications of repeat analysis on a genomic scale. A ubiquitous and conserved signal for RNA localization in chordates.

Curr Biol. Bao Z, Eddy SR. Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res. A clustering method for repeat analysis in DNA sequences. Genome Biol. Article Google Scholar. A fast algorithm for genome-wide analysis of proteins with repeated sequences.

George R a, Heringa J. Trends Biochem Sci. Mining microsatellites in eukaryotic genomes. Trends Biotechnol. Merkel A, Gemmell N.

Detecting short tandem repeats from genome data: Opening the software black box. Brief Bioinform. Review of tandem repeat search tools: a systematic approach to evaluating algorithmic performance.

Article PubMed Google Scholar. Hoffman C. Match patterns in A. Accessed 2 Nov A fast string searching algorithm. Commun ACM. Farach M. Prevalence and genetic diversity of Anaplasma marginale strains in cattle in South Africa. Zoonoses Public Health. Functional and immunological relevance of Anaplasma marginale major surface protein 1a sequence and structural analysis.

PLoS One. Association of Anaplasma marginale strain superinfection with infection prevalence within tropical regions. Genetic diversity of Anaplasma species major surface proteins and implications for anaplasmosis serodiagnosis and vaccine development. Anim Health Res Rev. Genetic diversity and molecular phylogeny of Anaplasma marginale isolates from Minas Gerais, Brazil. Vet Parasitol. Analysis of world strains of Anaplasma marginale using major surface protein 1a repeat sequences. Vet Microbiol.

Serologic and molecular characterization of Anaplasma species infection in farm animals and ticks from Sicily. Genetic diversity of major surface protein 1a of Anaplasma marginale in beef cattle. Epidemiology and evolution of the genetic variability of Anaplasma marginale in South Africa. Ticks Tick Borne Dis. Strain composition of the Ehrlichia Anaplasma marginale within persistently infected cattle, a mammalian reservoir for tick transmission. Detection of genetic diversity of Anaplasma marginale isolates in Minas Gerais, Brazil.

Rev Bras Parasitol Vet. Genetic diversity of Anaplasma marginale in Argentina. Interdiscip Sci Comput Life Sci 8, 75—83 Download citation. Received : 24 November Revised : 21 July Accepted : 22 July Published : 14 August Issue Date : March Anyone you share the following link with will be able to read this content:. Sorry, a shareable link is not currently available for this article.

Provided by the Springer Nature SharedIt content-sharing initiative. Skip to main content. Search SpringerLink Search. Abstract It has become clear that repetitive sequences have played multiple roles in eukaryotic genome evolution including increasing genetic diversity through mutation, changes in gene expression and facilitating generation of novel genes. References 1.