Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Manipulating multiple sequence alignments via MaM and WebMaM.

Can Alkan1, Eray Tüzün, Jerome Buard

  • 1Department of EECS, Case Western Reserve University, Cleveland, OH, USA.

Nucleic Acids Research
|June 28, 2005
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Rapid adaptive increase of amylase gene copy number in Indigenous Andeans.

Nature communications·2026
Same author

LCPAN: efficient variation graph construction using locally consistent parsing.

Genome biology·2026
Same author

GenCore: Genomic distance estimation using Locally Consistent Parsing.

bioRxiv : the preprint server for biology·2026
Same author

LCPan: efficient variation graph construction using Locally Consistent Parsing.

ArXiv·2025
Same author

Robust software development practices improve citations of RNA-seq tools.

bioRxiv : the preprint server for biology·2025
Same author

Population-level gene copy number variations reveal distinct genetic properties of different Malus species.

BMC genomics·2025
Same journal

Correction to 'scSuperAnnotator: A platform for benchmarking comparison and visualizing automated cellular annotation methods for scRNA-seq data'.

Nucleic acids research·2026
Same journal

Correction to 'Differentiable partition function calculation for RNA'.

Nucleic acids research·2026
Same journal

Deployment of non-canonical splicing in tunicate genomes is mediated by divergent U2AF function and changing m6A modification in U1 and U6 snRNA.

Nucleic acids research·2026
Same journal

Bacillus subtilis DnaB forms multiple protein-protein interactions essential for DNA replication initiation.

Nucleic acids research·2026
Same journal

Multiple forms of protein-protein and DNA binding are exhibited by BrxC from the BREX phage restriction system.

Nucleic acids research·2026
Same journal

Biosynthesis of glycosylated 5-hydroxycytosine in the DNA of diverse viruses.

Nucleic acids research·2026
See all related articles

MaM is a software tool for analyzing genomic sequence alignments. It precisely locates repeat elements, exons, and unique regions, aiding phylogenetic analysis in large-scale sequencing projects.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Analyzing multiple genomic sequence alignments is crucial for understanding DNA.
  • Identifying specific regions like repeats, exons, and unique sequences presents a computational challenge.

Purpose of the Study:

  • To introduce MaM, a software tool designed for processing and manipulating multiple genomic sequence alignments.
  • To facilitate the precise identification and extraction of specific genomic regions for further analysis.

Main Methods:

  • MaM processes multiple genomic sequence alignments.
  • It utilizes user-defined programs, databases, or tables to identify repeat elements, exons, and unique regions.
  • The tool extracts subalignments of these identified regions for independent or combined analysis.

Related Experiment Videos

Main Results:

  • MaM accurately computes the locations of common repeat elements, exons, and unique regions within aligned genomic sequences.
  • Graphical displays enable visualization of sequence variation across repeat, non-repeat, and coding regions.
  • Subalignments corresponding to these regions can be extracted for detailed study.

Conclusions:

  • MaM enhances the analysis of genomic sequence alignments by providing precise region identification and visualization.
  • The software supports phylogenetic analysis and processing of specific DNA segments in large-scale sequencing efforts.
  • MaM is freely available for non-commercial use, with a web interface (WebMaM) also provided.