example alignment #1 (fasta format)A. J. MuozPajares
Given the skate sequence in FASTA format >ENA|AF486831|AF486831.1 Raja erinacea Ser/Thr kinase STK mRNA, complete cds. : Location:1..1000 GGCGATGCTGCATGGAGCGGAGCAACGGCAACAGCAGCCGGAGGAGCCCGAGGAATCCGA GCCGATCCTGGCGGCTTTCAGAGACTATCTGGAGATGGACGAGGTGGTTGACTACATCAG ...
# defaultbedtoolsgetfasta-fireference.fasta-bedregions.bed-fooutput.fasta# Extract sequences using name columnbedtoolsgetfasta-fireference.fasta-bedregions.bed-fooutput.fasta-name# Extract sequences and strand informationbedtoolsgetfasta-s-fireference.fasta-bedregions.bed-fooutput.fasta Where, In additi...
# reference file in fasta format ref: 'Ref.fa' @@ -19,6 +19,6 @@ MIN_SUPPORT_CALLER: 2 # SV caller list to be used. Default is all 5 SV callers. Options: [sniffles, cuteSV, svim, pbsv, Assemblytics] SV_CALLER_LIST: [sniffles, cuteSV, svim, pbsv, Assemblytics] # Long rea...
-R: Reference genome,Input species reference genome sequence files, including fa, fna, and fasta formats. -gtf: Gene transfer format,Input species Gene transfer format files. Remove the-s: species_nameparameter in v1.0 New Output ann dir:It is used to store the result file after ANNOVAR sof...
Gene properties in the database can be accessed in two ways A Python script qimm.py (QueryIMMunome) was written as a command-line interface (CLI) to query data and output nucleotide and amino acid sequences in fasta format [40]. This script can be readily incorporated in ...
(i.e. a fasta file!) My objective is to identify a substring using its position, which is the second element of the first line (i.e., 10), and extract a certain number of positions around it, specifically 5 positions. EFGHIJKLMNO ...
("app.vep.cache.species"), "--fasta", pipelineOptions.getString("input.fasta"), "--fork", pipelineOptions.getString("app.vep.num-forks"), "-i", pipelineOptions.getString("vep.input"), "-o", "STDOUT", "--force_overwrite", "--offline", "--everything"); logger.debug("VEP ...
public GeneParser(Path geneDirectoryPath, Path genomeSequenceFastaFile, Species species, boolean flexibleGTFParsing, CellBaseSerializer serializer) { this(null, geneDirectoryPath.resolve("description.txt"), geneDirectoryPath.resolve("xrefs.txt"), geneDirectoryPath.resolve("idmapping_selected.tab.gz"),...
The sequence was submitted in Fasta format to the web-based software DOGMA (Dual Organellar Genome Annotator) [62] for primary annotation. BLAST searches were done on NCBI Blast Entrez databases to ensure the identity of PCGs and rRNA genes. To identify the tRNA genes in the genome, we used...