Results for "DB"
Bio-Scripts
Retrieve NCBI GenBank records with a range of accession numbers
...rch { my %param = @_; my $esearch = "$param{url}/esearch.fcgi?db=$param{database}" ....rettype=$param{returnType}&retmode=text&retstart=$retstart&retmax=$retmax&db=$param{database}&query_key=$q...2910 days ago
Blast script to index and extract sequence !!
...CACAGACAGATAAAAATTACAGAGTAC # generate the blast database $ makeblastdb -dbtype nucl -out EC -in EC4115.f...ACAGAC .... # query the blast database by id and coordinates $ blastdbcmd -db EC -range 100-105 -ent...2846 days ago
- ...quire v5.6.0; use GD; use DB_File; use strict; use vars...} } if (!defined $DB_File::VERSION || $DB_File::VE...ylen = $k; } # Close that DB dbmclose %DOT; #...} } %hash = (); } dbmclose %TEMPFILE; $img->rect...
2687 days ago
BASH script for SelfBLAST a genome
...mon settings FASTAFILE=MergedContigs.fasta MYDB=myDB OUTFILE=seeRES THREAD=20 S...ng this script $USER; Me creating creating blastDB named $MYDB for you"; make...BLASting"; blastn -task megablast -query $SEQ -db $MYDB -evalue 1e-5 -num_threa...2646 days ago
Extract fasta sequence from a multifasta file with coordinates
#!/usr/bin/perl use Bio::DB::Fasta; #USAGE perl extra...$querySizeED = shift; my $db = Bio::DB::Fasta->new( $fastaFile ); my @ids = $db->get_all_primary_ids; fore...n"; } __END__ use Bio::DB::Fasta; # Create databas...rimarySeqI. my $seq = $db->get_Seq_by_id('CHROMOSOME_I'...2527 days ago
Extract the fastq sequence with range in Perl
use Bio::DB::Fasta; open(POSITIONS,"positions.txt"); while(){ chomp; my ($seqName,$begin,$end) = split(/\s/); my $db = Bio::DB::Fasta->new('allGenomeContacted.fa'); my $seq = $db->seq("$seqName", $begin => $end); print "$seq\n"; } close(POSITIONS);2463 days ago
- # generate dotplot lastdb test/ref.fa lastal -f TAB test/ref.fa test/contigs.reduced.pacbio.fa | last-dotplot - test/contigs.reduced.pacbio.fa.ref.png lastal -f TAB test/ref.fa test/contigs.reduced.nanopore.fa | last-dotplot - test/contigs.reduced.nanopore.fa.ref.png
2246 days ago
Plot custom gene density with R
library(karyoploteR) pp2244 days ago
- ....24.1 App::cpanminus JSON::Parse XML::Parser XML::Simple LWP LWP::Simple LWP::Protocol::https Archive::Extract Archive::Tar Archive::Zip CGI DBI Time::HiRes DBD::mysql Encode File::Copy::Re...
2139 days ago
Perl script to convert GFF 2 FASTA !
...erl use strict; use warnings; use Bio::Seq; use Bio::SeqIO; use Bio::DB::Fasta; $| = 1; # Flush...promoter) ### First, index the genome my $file_fasta = $ARGV[0]; my $db = Bio::DB::Fasta->new($file_f...2133 days ago
