BLAST how to use blastn

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

$ makeblastdb.exe -h
USAGE
  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.exe

$ blastn -h
USAGE
  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