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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 terminates with a blank line. The format is deliberately quite dense.

Description

More detailed information about this field from each metasource.

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 terminates with a blank line. The format is deliberately quite dense.

metasource: Fairsharing.org
version: FAIRsharing.org: Chain Format for pairwise alignment; Chain Format for pairwise alignment; DOI: https://doi.org/10.25504/FAIRsharing.72e4we; Last edited: Jan. 8, 2019, 1:28 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

Webpage:

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

Webpage

More detailed information about this field from each metasource.

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

Tags:

Tags
More detailed information about this field from each metasource.

deoxyribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: Chain Format for pairwise alignment; Chain Format for pairwise alignment; DOI: https://doi.org/10.25504/FAIRsharing.72e4we; Last edited: Jan. 8, 2019, 1:28 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

sequence alignment
metasource: Fairsharing.org
version: FAIRsharing.org: Chain Format for pairwise alignment; Chain Format for pairwise alignment; DOI: https://doi.org/10.25504/FAIRsharing.72e4we; Last edited: Jan. 8, 2019, 1:28 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

region
metasource: Fairsharing.org
version: FAIRsharing.org: Chain Format for pairwise alignment; Chain Format for pairwise alignment; DOI: https://doi.org/10.25504/FAIRsharing.72e4we; Last edited: Jan. 8, 2019, 1:28 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

dna sequence alignment region

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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 ...

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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 ...

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The Sequence Alignment/Map (SAM) format is a TAB-delimited text format consisting of a header section, which is optional, and an alignment section.

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.

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 ...

Big Multiple Alignment Format

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Stockholm Multiple Alignment Format

The "Stockholm" format is a system for marking up features in a multiple alignment. These mark-up annotations are preceded by a 'magic' label, of which there are four types. The Stockholm format is us ...

CLUSTAL-W Alignment Format

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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 ...

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) ...

NCBI Trace Archives

The Trace Archives includes the following archives: The Sequence Read Archive (SRA) stores raw sequence data from "next-generation" sequencing technologies including 454, IonTorrent, Illumina, SOLiD, ...

nucleotide inFormation binary Format

The .nib format pre-dates the .2bit format and is less compact. It describes a DNA sequence by packing two bases into each byte.

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 ...

Standard Flowgram Format

Standard flowgram format (SFF) is a binary file format used to encode results of pyrosequencing from the 454 Life Sciences platform for high-throughput sequencing. SFF files can be viewed, edited and ...

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 ...

Gene Prediction File Format

Gene Prediction File Format (genePred) is a table format commonly used for gene prediction tracks in the Genome Browser. Variations of genePred include standard format, extended format and a format wh ...

BAliBASE

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

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.

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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