I have a FASTA file of a eukaryotic genome not in any database. I want to search it for sequences that belong to endosymbionts. I have the endosymbiont sequeces as seperate FASTA files. The endosymbiont sequences are very short (350-600 bp). Is there a tool for that?
Hi @AndyCarter
Just off hand, you could try using a BLAST+ tool.
- See the mapping tutorial here for how this works. → Sequence analysis / Tutorial List
- How to prepare your target custom genome fasta file. → FAQ: How to use Custom Reference Genomes?
I would suggest finding a publication that does what you are attempting to do. Most bioinformatics manipulations can be done in Galaxy, even if the exact tools from a particular publication are not hosted (are not open source or similar).
Hope this helps! 