For example: Chromosome, Contig, Scaffold. Will be created if not found. Here, we assume sub-directories for branches, e. About Download refseq-genomic data and prepare it for Kraken Resources Readme. MIT License. Releases No releases published. Packages 0 No packages published.
You signed in with another tab or window. GRCm38 Patch 6 - Sequence files. Multiple alignments of 29 vertebrate genomes with Mouse Conservation scores for alignments of 29 vertebrate genomes with Mouse Basewise conservation scores phyloP of 29 vertebrate genomes with Mouse FASTA alignments of 29 vertebrate genomes with Mouse for CDS regions. Multiple alignments of 16 vertebrate genomes with Mouse Conservation scores for alignments of 16 vertebrate genomes with Mouse.
Multiple alignments of 9 vertebrate genomes with Mouse Conservation scores for alignments of 9 vertebrate genomes with Mouse. Multiple alignments of 4 vertebrate genomes with Mouse Conservation scores for alignments of 4 vertebrate genomes with Mouse.
Multiple alignments of 8 vertebrate genomes with Opossum Conservation scores for alignments of 8 vertebrate genomes with Opossum. Multiple alignments of 6 vertebrate genomes with Opossum Conservation scores for alignments of 6 vertebrate genomes with Opossum.
Multiple alignments of 7 vertebrate genomes with Orangutan Conservation scores for alignments of 7 vertebrate genomes with Orangutan. Multiple alignments of 5 vertebrate genomes with Platypus Conservation scores for alignments of 5 vertebrate genomes with Platypus. Multiple alignments of 19 vertebrate genomes with Rat Conservation scores for alignments of 19 vertebrate genomes with Rat Basewise conservation scores phyloP of 19 vertebrate genomes with Rat FASTA alignments of 19 vertebrate genomes with Rat.
Multiple alignments of 12 vertebrate genomes with Rat Conservation scores for alignments of 12 vertebrate genomes with Rat Basewise conservation scores phyloP of 12 vertebrate genomes with Rat. Multiple alignments of 8 vertebrate genomes with Rat Conservation scores for alignments of 8 vertebrate genomes with Rat.
Multiple alignments of 8 vertebrate genomes with Stickleback Conservation scores for alignments of 8 vertebrate genomes with Stickleback. Multiple alignments of 19 mammalian 16 primate genomes with Tariser Conservation scores for alignments of 19 mammalian 16 primate genomes with Tarsier Basewise conservation scores phyloP of 19 mammalian 16 primate genomes with Tarsier FASTA alignments of 19 mammalian 16 primate genomes with Tarsier for CDS regions.
Multiple alignments of 10 vertebrate genomes with X. Multiple alignments of 8 vertebrate genomes with X. Multiple alignments of 6 vertebrate genomes with X. Multiple alignments of 4 vertebrate genomes with X. Multiple alignments of 7 genomes with Zebrafish Conservation scores for alignments of 7 genomes with Zebrafish Basewise conservation scores phyloP of 7 genomes with Zebrafish.
Tropicalis xenTro2. Multiple alignments of 5 vertebrate genomes with Zebrafish Conservation scores for alignments of 5 vertebrate genomes with Zebrafish. Multiple alignments of 6 vertebrate genomes with Zebrafish Conservation scores for alignments of 6 vertebrate genomes with Zebrafish. The data will download as a file with tar compression. Accessing individual RefSeq genome records for viruses not organized in individual assemblies NCBI creates an individual RefSeq sequence record for each viral segment.
Use the links under the Explore Viral Genome Sequences section of the Viral Genomes page a part of Genome resource for convenient access and selection of the data that you want: Select a browser, for example the Viral genome browser. All genomes assemblies linked to a particular BioProject can be downloaded using the genome download service in the Assembly resource described above. We changed the sequence identifier format in the FASTA files to make our datasets more usable by the community.
This format provides more information but requires that the individual sequence identifiers be parsed out of the compound string. K substr. Providing sequence and annotation files with matching sequence identifiers supports their use in commonly used RNA-Seq analysis packages and in other analysis pipelines that rely on simple string comparison to match sequence identifiers.
Certain symbols and punctuation marks have a special meaning to computer operating systems, consequently, they can cause problems if they are included as part of directory or file names. Examples include spaces, , , [, ] and '.
Whenever one or more of these special characters appears in the organism name they are replaced by an underscore. Taxonomy places square brackets around the genus for some species to indicate that they are misclassified.
The current names continue to be used with square brackets until the species has been formally renamed. The square brackets around the genus are converted to underscores when a directory name is created for one of these misclassified species resulting in a directory name that begins with an underscore.
Repetitive sequences in eukaryotic genome assembly sequence files, as identified by WindowMasker , have been masked to lower-case.
The location and identity of repeats found by RepeatMasker are also provided in a separate file. These spans could be used to mask the genomic sequences if desired. Be aware, however, that many less studied organisms do not have good repeat libraries available for RepeatMasker to use. Alignment programs typically have parameters that control whether the program will ignore lower-case masking, treat it as soft-masking i.
The program's documentation should indicate the default behavior. To have blastn treat lower-case masking in the query sequence as soft-masking add:. Here are two examples of commands that will convert lower-case masking to masking with Ns hard-masked :. The Firefox web browser is unable to display long FTP directory and file names in http mode. Many FTP clients have incomplete implementation of the FTP symbolic link specification or other bugs causing them to incorrectly treat symbolic links as files or directories.
This may lead to the following problems:. National Center for Biotechnology Information , U. What is the easiest way to download data for multiple genome assemblies? What is the best protocol to use to download large data sets? Are files on the FTP site updated following annotation updates? My organism of interest is available in both GenBank and RefSeq. Is the genome the same?
Which one should I use? How are the FTP directories structured? What is the file content within each specific assembly directory? How can I find the sequence and annotation of my genome of interest? Where can I find information to help me chose between the many different assemblies for a species?
How can I download only the current version of each assembly? How can I download RefSeq data for all complete bacterial genomes? How can I download all genome assemblies from the Human Microbiome Project, or other project? Why do some species directory names start with an underscore? Do you provide assembly data formatted for use by sequence read alignment pipelines?
Are repetitive sequences in eukaryotic genomes masked?
0コメント