[BiO BB] Running BLAST with a new scoring matrix

[Bossers, Alex]

Achu,
Have a look at the NCBI blast+ documentation (snippet below). It will allow what you want I guess;
The -matrix option.
Alex

$ blastx -help
USAGE
  blastx [-h] [-help] [-import_search_strategy filename]
    [-export_search_strategy filename] [-db database_name]
    [-dbsize num_letters] [-gilist filename] [-seqidlist filename]
    [-negative_gilist filename] [-entrez_query entrez_query]
    [-db_soft_mask filtering_algorithm] [-db_hard_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]
    [-xdrop_ungap float_value] [-xdrop_gap float_value]
    [-xdrop_gap_final float_value] [-searchsp int_value]
    [-frame_shift_penalty frameshift] [-max_intron_length length]
    [-seg SEG_options] [-soft_masking soft_masking] [-matrix matrix_name]
    [-threshold float_value] [-culling_limit int_value]
    [-best_hit_overhang float_value] [-best_hit_score_edge float_value]
    [-window_size int_value] [-ungapped] [-lcase_masking] [-query_loc range]
    [-strand strand] [-parse_deflines] [-query_gencode int_value]
    [-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
   Translated Query-Protein Subject BLAST 2.2.25+
Use '-help' to print detailed descriptions of command line arguments
----------------------

THis should do it:
 -matrix <String>
   Scoring matrix name (normally BLOSUM62)


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________________________________________
Van: bbb-bounces at bioinformatics.org [bbb-bounces at bioinformatics.org] namens Dr. Achuthsankar S. Nair [sankar.achuth at gmail.com]
Verzonden: vrijdag 29 juli 2011 6:10
Aan: bbb at bioinformatics.org
Onderwerp: [BiO BB] Running BLAST with a new scoring matrix

Hi
I have developed a new scoring matrix to replace PAM, can anyone suggest how
we can test this out in alignment tools inclusing BLAST ?
Is there a tool which accepts user defined  scoring matrix ?
Thanks in advance
Achu

--

Dr Achuthsankar S Nair
Director, State Inter-University  Centre for Bioinformatics
University of Kerala, Trivandrum 695581, INDIA
Tel (O) 471-2308759 (R) 471-2542220
www.cbi.keralauniversity.edu
www.achu.keralauniversity.edu
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