What does MAF mean in UNCLASSIFIED

Definition

Multiple Alignment Format (MAF) is a text-based format used to store multiple nucleic acid or protein sequences in a single file or database. Sequences are stored with annotations that provide information about where each part of the sequence came from. This makes it easy for researchers to compare sequences from different sources or between species. The information stored within MAF files can be visualized in many ways such as dot plots, pairwise alignments, and multiple alignment views.

Uses

The primary use of MAF files is for analyzing genome and transcriptome data produced by next-generation sequencing techniques such as whole-genome/exon sequencing projects (WGS/WES). As more organism genomes become available to researchers, the need for efficient storage and comparison methods simultaneously becomes increasingly important. MAF files allow researchers to easily access related DNA sequences from different species stored together in one place instead of accessing individual databases separately. They can also be used to reconstruct evolutionary relationships between species by comparing sequences with those collected from other organisms.

Benefits

The primary benefit of using MAF files is that they offer greater flexibility when studying gene and protein interactions than other formats such as FASTA files and BLAST output formats. The inclusion of annotations allows researchers to quickly isolate specific regions of interest within alignments without having to redo computationally expensive analyses every time new data becomes available. Additionally, visualization tools like UCSC’s Genome Browser allow users to easily visualize aligned sequences stored within MAF files as well as query data with comparative genomics approaches such as conservation scores.