I made a protein database using diamond makedb and then a blastx using a nucleotide query. First the makedb data doesn't show actual amino acid sequences but hidden/unknown characters. Should this be the case? See example below
mî¤øJV w ÿ
ÿ(AGly)Aac:AJ628983:1985-2539:555 ÿ
ÿ(AGly)Aac2-Ia:L06156:264-800:537 ÿ
ÿ(AGly)Aac2-Ib:U41471:266-822:588 ÿ
ÿ(AGly)Aac2-Ic:U72714:373-918:546 ÿ
ÿ(AGly)Aac(2')-Id:U72743:386-1018:533 ÿ
ÿ(AGly)Aac2-Ie:NC_011896:3039059-3039607:549 ÿ
ÿ(AGly)Aac3-I:AJ877225:5293-5757:465 ÿ
ÿ(AGly)Aac-IIIa:X55652:1124-1939:816 ÿ
Secondly, Diamond alignment show no output.
Summary and Output looks like this:
XML data formatxmldatabase? diamond v0.8.24.86 | by Benjamin Buchfink buchfink@gmail.com Check http://github.com/bbuchfink/diamond for updates.
CPU threads: 1
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Target sequences to report alignments for: 2
<blastoutput> <blastoutput_program>blastx</blastoutput_program> <blastoutput_version>diamond 0.8.24</blastoutput_version> <blastoutput_reference>Benjamin Buchfink, Xie Chao, and Daniel Huson (2015), "Fast and sensitive protein alignment using DIAMOND", Nature Methods 12:59-60.</blastoutput_reference> <blastoutput_db></blastoutput_db> <blastoutput_query-id>Query_1</blastoutput_query-id> <blastoutput_query-def>10404.P712T2a_0_F/1</blastoutput_query-def> <blastoutput_query-len>422</blastoutput_query-len> <blastoutput_param> <parameters> <parameters_matrix>BLOSUM62</parameters_matrix> <parameters_expect>0.001</parameters_expect> <parameters_gap-open>11</parameters_gap-open> <parameters_gap-extend>1</parameters_gap-extend> <parameters_filter></parameters_filter> </parameters> </blastoutput_param> <blastoutput_iterations> </blastoutput_iterations> </blastoutput>
Is this because there are no blast hits to display? I previously had hits with the same datasets. Also, why isn't there local blastn on galaxy by default as it is such a commonly used programme? Why does it have to be added on by user?
Thank you for your help.
