Results for "query"
Bio-Scripts
...options: 0 = pairwise, 1 = query-anchored showing identities,...d, show identities, 4 = flat query-anchored, no identities, 5 =...default = 0 -F Filter query sequence with SEG [String]...SeqAlign file ('Believe the query defline' must be TRUE) [File...1002 days ago
Run Pango on your multifasta file !
...ova_all_samples_combined.fa (pangolin) [jnarayan@hn1 FASTA]$ pangolin Input_for_Cova_all_samples_combined.fa All dependencies satisfied. The query file is:/home/jnarayan/RF_DAT...939 days ago
Script to rapid genome clustering based on pairwise ANI
...from blast+ package to perform all-vs-all blastn of sequences: blastn -query -db -outfmt '6 std qlen sle...ntity flag will speed up the search at the cost of sensitivity: blastn -query -db -outfmt '6 std qlen sle...687 days ago
- (jitENV) [jnarayan@hn1 preetiDATA]$ blastn -task blastn -query list_flank_0.fa -subject ../monkeypoxDATA_07_06_22/JIT_gisaid_pox_2022_09_06_07.fasta -evalue 20000000 -word_size 5 -num_threads 4 -outfmt 6 -out blastn_0.txt -qcov_hsp_perc 100 -perc_identity 100 -max_target_seqs 10000
644 days ago
Identify genome-wide synteny with LASTZ alignment
....synnet.axt AAChr1.txt.sizes FFChr1.txt.sizes -tPrefix=target. -qPrefix=query. chr1.chain.filter.tnet.synne...l Maf2rawsynteny.pl chr1.chain.filter.tnet.synnet.axt.maf target.AAChr1 query.FFChr1 perl Get_synteny.pl...569 days ago
Perl script to parse blast results and plot basic stats !
...print "---------------------------\n"; # Print detailed information for each entry for my $entry (@blast_entries) { print "Query: ", $entry->{QUERY}, "\n"; print "S...146 days ago
Python script to finds extact similar sequence between two multi fasta files !
...ort sys def perform_local_blast(query_file, subject_file, output_fi...astn_cline = NcbiblastnCommandline(query=query_file, subject=subject_f...= fields[0] # Extract the aligned query sequence (qseq)...cal BLAST perform_local_blast(query_file, subject_file, output_fi...55 days ago
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