<div dir="ltr"><div><div>Thanks. Yes, I should use "-max_hsps".<br><br></div>Best<br></div>Quanwei<br></div><div class="gmail_extra"><br><div class="gmail_quote">2017-02-13 9:02 GMT-05:00 Michael Campbell <span dir="ltr"><<a href="mailto:michael.s.campbell1@gmail.com" target="_blank">michael.s.campbell1@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Quanwei,<br>
<br>
Different versions/implementations of blast do have parameters. Based on the usage you posted my guess is that the parameter you want is “-max_hsps”<br>
<br>
Thanks,<br>
Mike<br>
<div><div class="h5">> On Feb 10, 2017, at 11:53 PM, Quanwei Zhang <<a href="mailto:qwzhang0601@gmail.com">qwzhang0601@gmail.com</a>> wrote:<br>
><br>
> Hello:<br>
><br>
> I want to assign gene function to the predicted genes. I collected UniProt/SwissProt human, mouse and rat protein sequences (including both canonical and isoforms). Then use "makeblastdb" to build the database. And then run "blastp -db ... -max_hsps_per_subject 1" following the example in the protocol. But it returns me an error: Unknown argument: "max_hsps_per_subject".  Why this happens? Is it because I am using a different version of blastp?<br>
><br>
> USAGE<br>
>   blastp [-h] [-help] [-import_search_strategy filename]<br>
>     [-export_search_strategy filename] [-task task_name] [-db database_name]<br>
>     [-dbsize num_letters] [-gilist filename] [-seqidlist filename]<br>
>     [-negative_gilist filename] [-entrez_query entrez_query]<br>
>     [-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm]<br>
>     [-subject subject_input_file] [-subject_loc range] [-query input_file]<br>
>     [-out output_file] [-evalue evalue] [-word_size int_value]<br>
>     [-gapopen open_penalty] [-gapextend extend_penalty]<br>
>     [-qcov_hsp_perc float_value] [-max_hsps int_value]<br>
>     [-xdrop_ungap float_value] [-xdrop_gap float_value]<br>
>     [-xdrop_gap_final float_value] [-searchsp int_value]<br>
>     [-sum_stats bool_value] [-seg SEG_options] [-soft_masking soft_masking]<br>
>     [-matrix matrix_name] [-threshold float_value] [-culling_limit int_value]<br>
>     [-best_hit_overhang float_value] [-best_hit_score_edge float_value]<br>
>     [-window_size int_value] [-lcase_masking] [-query_loc range]<br>
>     [-parse_deflines] [-outfmt format] [-show_gis]<br>
>     [-num_descriptions int_value] [-num_alignments int_value]<br>
>     [-line_length line_length] [-html] [-max_target_seqs num_sequences]<br>
>     [-num_threads int_value] [-ungapped] [-remote] [-comp_based_stats compo]<br>
>     [-use_sw_tback] [-version]<br>
><br>
>  Thanks<br>
> Best<br>
> Quanwei<br>
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</blockquote></div><br></div>