xml file import in omicsbox blast2go and daa files in megan

Question

[sunettevos5]

Good day

I am trying to import xml files in Omicx box blast2go for functional mapping and annotations. I have even tried DAA files in Megan to map to pathways with no luck. However, after import, the xml file is empty, which according to the size of these files is not the case. I have tried changing the import parameters, but I do not have a lot of options to change. There is no option to change the separator and position etc. as mentioned on their support website as a solution to this. Have anyone used the blast2go in Omicsbox with xml files. How do I get my xml files imported without getting an empty file? Secondly if anyone perhaps also know how to use DAA files in Megan to get functional annotations, as I only get taxonomic annotations, all the functional annotations are classified as unknown. Any help will be appreciated as I already tried the websites for blast2go and Megan, but I cannot find a way to solve my problem?

Regards Sunette

Answer 1

[sgoetz123]

Hi.
The XML files you need for importing blast results in OmicsBox to perform functional annotation with the Blast2GO methodology need to have specific formatting to be able to be used correctly (you can not use megan files for this). This is important because the IDs of the blast hits have to be parsed and matched with the gene ontology before the functional annotation can be done. http://docs.blast2go.com/user-manual/gene-ontology-mapping/

The format has to be the NCBI Blast XML2 format with command line parameter "-outfmt 14". Please see: https://www.ncbi.nlm.nih.gov/books/NBK279684/

Once you sequences are blasted against a protein database with the NCBI Blast blastx you can use the XML files in OmcisBox/Blast2GO.

If you want to blast against a custom database and have to create your own OmicsBox has a tool for this and it allows to also annotate with taxonomic IDs to your query database. https://www.biobam.com/taxonomic-mapping-file-make-blast-database-within-omicsbox/

Answer 2

[jaredbernard]

Is there a way to either merge xml outputs of blast, or load multiple blast results in Blat2GO/OmicsBox?

I have blast results via Swissprot and nr and need to load both, but when I try to load a second set of blast results, it simply replaces the first. I have tried selecting "skip" or "replace" with no luck.

I've also tried merging the .box/.b2g files by trying "add", "skip", or "replace" -- I can get a combined table that shows all results blasted, but not their descriptions.