Download a genetic sequence from ucsc genome browser

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Connect and share knowledge within a single location that is structured and easy to search. If I have genome coordinates is there a simple way to download the entire intervening sequence from the UCSC genome browser? I found some fancy way of using ftp but I can't figure it out.

I did find a way of doing this using UCSC das. If the pertinent info is changed in the page address here, it will output the intervening sequence between two locations:. Table browser allows you to do that. In the dropdown box called output format select sequence and click the button named get output.

You'll get the sequence. Actually Table browser is quite useful as you can get different kinds of data for a given genomic region which include annotations, variation, transcription factor binding sites etc.

Sign up to join this community. The best answers are voted up and rise to the top. Stack Overflow for Teams — Collaborate and share knowledge with a private group. The Genome Browser downloads site provides prepackaged downloads of bp, bp, and bp upstream sequence for RefSeq genes that have a coding portion and annotated 5' and 3' UTRs.

You can obtain these from the bigZips downloads directory for the assembly of interest. To fetch the upstream sequence for a specific gene, use the Table Browser. Enter the genome, assembly, and select the knownGene table. Paste the gene name or accession number in the identifier field.

Choose sequence for the output format type, then click the get output button. On the next page, select genomic. On the final page, you will have the opportunity to configure the amount of upstream promoter sequence to fetch, along with several other options.

Click Get Sequence when you've finished configuring the output. You can also use the Genome Browser to obtain sequence for a specific gene.

Open the Genome Browser window to display the gene in which you're interested. Alternatively, you can click the DNA link in the top menu bar of the Genome Browser tracks window to access options for displaying the sequence.

The conservation score data are stored in a group of tables in the annotation database downloads directory. The naming conventions of the tables vary among releases. Is this alignment on the minus strand? Minus strand coordinates in axt files are handled differently from how they are handled in the Genome Browser. To convert axt minus strand coordinates to Genome Browser coordinates, use:.

See an explanation of coordinate transforms in the genomeWiki. To determine the location of a specific marker, look up the marker's name in the stsAlias table to determine the UCSC ID assigned to the marker, and then use this ID to look it up in the stsMap table where the marker is located. You can obtain this information from the combination of a couple of tables.

This file also contains information about the position on the genome-wide maps, including the deCODE map. A second file, stsInfo2, contains additional information about each marker, including aliases, primer sequence information, etc.

This table is related to the first table by an ID the identNo field in both files. The fourth column of the BED output contains a lot of information separated by underscores.

For example:. The raw data underlying a track can be explored interactively with the Table Browser , Data Integrator , or Variant Annotation Integrator. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range using one of the hgdownload servers, example:.

Read more in our blog about Accessing the Genome Browser Programmatically to acquire data. How do I download dbSNP data? For versions dbSNP and above, the data is formatted in bigBed files.

Previous versions are MySQL tables. For automated analysis, the track data files can be downloaded from the downloads server for hg19 and hg Below are specific examples for dbSNP , however, the same methods and directories will work by substituting a more recent dbSNP release. Several utilities for working with bigBed-formatted binary files can be downloaded here. Run a utility with no arguments in order to see a brief description of the utility and its options.

With the -as option, the output includes an autoSql definition of data columns, useful for interpreting the column values. Output can be restricted to a particular region by using the -chrom, -start and -end options. See our searchable mailing list archives for more information and example queries.

We also have information on our blog about Accessing the Genome Browser Programmatically to acquire data. When using the SNP tracks, some records may contain information about one or more alleles instead of the usual two alleles for the SNP. The following information should explain how this is possible.

For simplicity, GTF files have been generated using the genePredToGtf method described above and are available on our download server for the main gene transcript sets.

For example, the hg38 GTF files. Tables are not stored in GTF as it would require many rows to describe a single transcript since each gene feature i. Download the genePredToGtf operating system-specific command-line utility from the utilities directory. The genePredToGtf utility can convert files from several sources, such as Table Browser output from a genePred table, a local downloaded gene set table like refGene.

Most of our tables have a special first column called "bin" that helps with quickly displaying data on the Genome Browser. This chrom,bin index causes query results to be ordered first by bin, then by chromStart. This allows us to query and return results more quickly than if they were sorted by chromStart. In order for your computer to run a freshly downloaded utility, you will need to update the file system permissions to allow your operating system to run the program.

Some data is provided by external groups and is not available for download or mirroring by any third party without the permission of the owners, such as the OMIM track data, which is the property of Johns Hopkins University.

For some tools, such as attempting a getData fetch with our API of restricted tracks, a 'Forbidden' error will be returned. Please email our private internal genome-www soe. Information on what is contained in each specific assembly analysis set can be found in the README by clicking the Genome sequence files link for the assembly of interest in our Downloads page.

JavaScript is disabled in your web browser You must have JavaScript enabled in your web browser to use the Genome Browser. Why doesn't this SNP have two alleles? The tables below previously found per assembly can now be downloaded from the hgFixed database : author cds cell description development gbCdnaInfo gbExtFile gbLoaded.

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