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FAIRsharing.c9fakh; Last edited: Jan. 8, 2019, 1:33 p.m.; Last accessed: Jan 03 2022 7:12 p.m.

Other names: bigPsl

Names

More detailed information about this field from each metasource.

Big Pattern Space Layout

metasource: Fairsharing.org
version: FAIRsharing.org: bigPsl; Big Pattern Space Layout; DOI: https://doi.org/10.25504/FAIRsharing.c9fakh; Last edited: Jan. 8, 2019, 1:33 p.m.; Last accessed: Jan 03 2022 7:12 p.m.

bigPsl

The bigPsl format stores alignments between two sequences just as PSL files do; however, bigPsl files are compressed and indexed as bigBeds. PSL files are converted to bigPsl files using the program bedToBigBed, run with the -as option to pull in a special autoSql (.as) file that defines the fields of the bigPsl.

Description

More detailed information about this field from each metasource.

The bigPsl format stores alignments between two sequences just as PSL files do; however, bigPsl files are compressed and indexed as bigBeds. PSL files are converted to bigPsl files using the program bedToBigBed, run with the -as option to pull in a special autoSql (.as) file that defines the fields of the bigPsl.

Webpage:

http://genome.ucsc.edu/goldenPath/help/bigPsl.html

Webpage

More detailed information about this field from each metasource.

http://genome.ucsc.edu/goldenPath/help/bigPsl.html

Tags:

Tags
More detailed information about this field from each metasource.

multiple sequence alignment
metasource: Fairsharing.org
version: FAIRsharing.org: bigPsl; Big Pattern Space Layout; DOI: https://doi.org/10.25504/FAIRsharing.c9fakh; Last edited: Jan. 8, 2019, 1:33 p.m.; Last accessed: Jan 03 2022 7:12 p.m.

multiple sequence alignment

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Big Chain

The bigChain format describes a pairwise alignment that allow gaps in both sequences simultaneously, just as chain files do; however, bigChain files are compressed and indexed as bigBeds. Chain files ...

Big Multiple Alignment Format

The bigMaf format stores multiple alignments in a format compatible with MAF files, which is then compressed and indexed as a bigBed. The bigMaf files are created using the program bedToBigBed, run wi ...

Big Browser Extensible Data Format

The bigBed format stores annotation items that can either be simple, or a linked collection of exons, much as BED files do. BigBed files are created initially from BED type files, using the program be ...

Big Gene Prediction

The bigGenePred format stores annotation items that are a linked collection of exons, much as BED files indexed as bigBeds do. However, the bigGenePred format includes 8 additional fields that contain ...

net alignment annotation Format

The net file format is used to describe the axtNet data that underlie the net alignment annotations in the Genome Browser.

Axt Alignment Format

Axt Alignment files are produced from Blastz, an alignment tool available from Webb Miller's lab at Penn State University. The axtNet and axtChain alignments are produced by processing the alignment f ...

Binary Alignment Map Format

BAM is the compressed binary version of the Sequence Alignment/Map (SAM) format, a compact and indexable representation of nucleotide sequence alignments. Many next-generation sequencing and analysis ...

bigWig Track Format

The bigWig format is for display of dense, continuous data that will be displayed in the Genome Browser as a graph. The bigWig files are in an indexed binary format. The main advantage of this format ...

BLAST-like Alignment Tool Format

BLAT is a multiple algorithms developed for the analysis and comparison of biological sequences such as DNA, RNA and proteins.

Chain Format for pairwise alignment

The chain format describes a pairwise alignment that allow gaps in both sequences simultaneously. Each set of chain alignments starts with a header line, contains one or more alignment data lines, and ...

Multiple Alignment Format

The Multiple Alignment Format stores DNA level multiple alignments in an easily readable format between entire genomes. Unlike previous formats this resource can cope with forward and reverse strand d ...

BEDgraph

The bedGraph format allows display of continuous-valued data in track format. This display type is useful for probability scores and transcriptome data. This track type is similar to the wiggle (WIG) ...

Wiggle Track Format

The wiggle (WIG) format is an older format for display of dense, continuous data such as GC percent, probability scores, and transcriptome data. The bigWig format is the recommended format for almost ...

UCSC Genome Browser database

Genome assemblies and aligned annotations for a wide range of vertebrates and model organisms, along with an integrated tool set for visualizing, comparing, analyzing and sharing both publicly availab ...

Encyclopedia of DNA Elements at UCSC

Encyclopedia of DNA Elements (ENCODE) has created a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory eleme ...

Binary sequence information Format

A .2bit file stores multiple DNA sequences (up to 4 Gb total) in a compact randomly-accessible format. The file contains masking information as well as the DNA itself. The DNA sequence is represented ...

BAliBASE

BAliBASE; a benchmark alignment database, including enhancements for repeats, transmembrane sequences and circular permutations.

Multiple Alignment using Fast Fourier Transform

MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program which implements the Fast Fourier Transform (FFT) to optimise protein alignments based on th ...

Personal Genome SNP Format

This format is for displaying SNPs from personal genomes. It is the same as is used for the Genome Variants and Population Variants tracks.

Pairs file format

A standard text format for pairs of genomic loci given as 1bp point positions, applicable to chromosome conformation experiments. Pairs files are produced as intermediate files in most Hi-C analysis p ...

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Data is amalgamated and only retrieved periodically.
Some of the resources used by the system:

® FAIRsharing.org
® Bioontology/Bioportal Terms
® Nucleic Acid Research - Database
® re3data.org
® bio.tools
® PubMed - Courtesy of the U.S. National Library of Medicine