BLAST how to use blastn
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http://davetang.org/wiki/tiki-index.php?page=BLAST
BLAST
BLAST
To download find the latest files here: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
Making your own blast databases to blast against
So after years of using formatdb, it has been replaced. To make a blast database using the new toolset:
$ makeblastdb.exe -hUSAGE makeblastdb.exe [-h] [-help] [-in input_file] [-dbtype molecule_type] [-title database_title] [-parse_seqids] [-hash_index] [-mask_data mask_data_files] [-out database_name] [-max_file_sz number_of_bytes] [-taxid TaxID] [-taxid_map TaxIDMapFile] [-logfile File_Name] [-version]DESCRIPTION Application to create BLAST databases, version 2.2.23+
To make a blast database:
makeblastdb.exe -in some_fasta.fa -dbtype nucl -title some_name -out database
Blasting short sequences
$ blastn -hUSAGE blastn [-h] [-help] [-import_search_strategy filename] [-export_search_strategy filename] [-task task_name] [-db database_name] [-dbsize num_letters] [-gilist filename] [-negative_gilist filename] [-entrez_query entrez_query] [-db_soft_mask filtering_algorithm] [-subject subject_input_file] [-subject_loc range] [-query input_file] [-out output_file] [-evalue evalue] [-word_size int_value] [-gapopen open_penalty] [-gapextend extend_penalty] [-perc_identity float_value] [-xdrop_ungap float_value] [-xdrop_gap float_value] [-xdrop_gap_final float_value] [-searchsp int_value] [-penalty penalty] [-reward reward] [-no_greedy] [-min_raw_gapped_score int_value] [-template_type type] [-template_length int_value] [-dust DUST_options] [-filtering_db filtering_database] [-window_masker_taxid window_masker_taxid] [-window_masker_db window_masker_db] [-soft_masking soft_masking] [-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value] [-best_hit_score_edge float_value] [-window_size int_value] [-off_diagonal_range int_value] [-use_index boolean] [-index_name string] [-lcase_masking] [-query_loc range] [-strand strand] [-parse_deflines] [-outfmt format] [-show_gis] [-num_descriptions int_value] [-num_alignments int_value] [-html] [-max_target_seqs num_sequences] [-num_threads int_value] [-remote] [-version]DESCRIPTION Nucleotide-Nucleotide BLAST 2.2.23+
blastn.exe -task blastn-short -db test -query interest.fa
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