Question: Diamond makedb and Diamond alignment
gravatar for linoya
24 days ago by
linoya0 wrote:

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 Check 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.

ADD COMMENTlink modified 24 days ago by Jennifer Hillman Jackson24k • written 24 days ago by linoya0
gravatar for Jennifer Hillman Jackson
24 days ago by
United States
Jennifer Hillman Jackson24k wrote:


The index is in binary format, so that is correct.

The XML output report does state there were no hits (there would be more content describing alignments, when there are any). Outputting tabular or SAM format instead can confirm this.

I retested Diamond/Index builder today and all is functioning correctly at Galaxy Main

Public servers may or may not have all the tools you want to use. For your own local Galaxy, most tools will need to be installed from the Tool Shed. The few tools that are in the Galaxy release distributions are a special class of utilities closely integrated with the primary application.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 24 days ago by Jennifer Hillman Jackson24k
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