Microsatellites are often referred to as short tandem repeats (STRs) by forensic geneticists and in genetic genealogy, or as simple sequence repeats (SSRs) by plant geneticists.
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Repeats. Repetitive sequence is found throughout genomes. It is important to mask repeats before gene annotation, as repeats will cause non-specific gene hits. You can also download repeat-masked sequence from our FTP site, either Download a sequence or region. Click on the 'Export data' button in the lefthand menu of most pages to export: FASTA sequence; GTF or GFF features. 23 Feb 2010 I want to use the complete FASTA format sequence as the reference genome to Do not use the repeat-mapped sequences ("_rm" in the filenames). It seems convenient to download the file denoted "toplevel", as it contains A new RepeatMasker package, Repeat Protein Database, and RepBase The new RepBase RepeatMasker-edition is available for download at: http://www.girinst.org. Introducing Dfam_consensus - Dfam's consensus sequence twin The following form facilitates extraction of short lengths of repeat sequence like to download the raw annotations for the entire genome, *.out and *.align files can Megabat - Jul 2008 - pteVam1, Mouse - Dec 2011 - mm10, Mouse - July 2007 - "masked genomic sequence" returns fasta formatted data from the assembly
R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops Piroon Jenjaroenpun. 1. We also analyzed genomic data of selected model organisms including Mus musculus (mm10), Rattus norvegicus (rn5), BED file and FASTA file (Figure 1C.iii). e. Download FASTA-file and feature-color-file to create publication graphics. For each sequence in the results section we offer a download of the FASTA-file and feature-color-file with the binding sites. Both files can be used in Jalview to create custom visualizations of the results. By using our site, you acknowledge that you have read and understand our Particular Inputs for promoter test Required Input for promoter test. The target promoters can be defined in two ways: A gene list, which contains gene symbols or Ensembl IDs, one gene per line in plain text format. Particular Inputs for promoter test Required Input for promoter test. The target promoters can be defined in two ways: A gene list, which contains gene symbols or Ensembl IDs, one gene per line in plain text format.
STAR had to be run directly because the bcbio upgrade command that made use of it kept stalling ( bcbio_nextgen.py upgrade –data –genomes GRCh37 –aligners bwa –aligners star). We have no idea why this made a difference but at least the direct STAR run could make use of multiple cores whereas the bcbio installer only uses 1
