Question regarding FASTA file gene name retrieval

[juliesoelberg]

Hi,

Thank you for the really nice software! I do have an issue with getting proper gene names out from a FASTA file, and have not been able to find any information regarding how the gene name is retrieved from the FASTA file.

My FASTA is generated from some WGS data we have.

FASTA example:

Trichophyton|32|FUN_000001-T1|NA|hypothetical protein|COG:E|||EC:4.3.1.18|PF14031,PF01168|IPR026956,IPR001608,IPR042208,IPR029066 MTSNIAYQPTAEVADLKALYVGRMLQDVDGPKPVIDREVARRNCQVMLDAALALNVEFRAHVKTHKTTELTRFQVGERSDTVRLVASTLVEAEQLVPFMKECQTKGRKVDLIYGLPVQPSCFPRLAELGKALGHGAVTCLVDSVDIVPFLSRYHALCGKRLGVFIKLDTGYGRAGVTYSSAQFNAIVSELYALEGKEPHLFTLRGFYSHMGHSYGSNNPSEAMDYLRTEIEGCKLAADRASAIPPPTPFDGETNYSQRRFVLSVGATPSTTAAQNLTGHETLSLPGADKAKDLIDQTKQKYDIELHAGAYVTLDMQQLAARARPNTSHLSFDDLALTVLAEVGSLYMHREHPEALVACGSLAIGREPCRSYKGWGVVTPWREQQQANDAAPAADERVGFYNPDGDKTGWILDRVSQEHGILRWHGSRQNMRPLRIGEKLRIWPNHCCICLAGFTYVLVVDSTAQGSEKDRIVDVWQSWRGW Trichophyton|32|FUN_000002-T1|NA|hypothetical protein|COG:J|||||IPR035959,IPR006175 MSAKRAVFTDKAPAPLPVFSQAIVHNGIVYCSGQVGTDPATRELVEGTVKDRTRWRDWDDGGLDRHRMVIDDVLTYREQAQIFRNITAVLEAAGSSLEKLLKVNIFLTNMDDFAAVNDVYAQVLNFEPKPVRTCVAVKTLPRNTDVEIECSAYI

Output example: Genes (L-kynurenine (Si)-synthase|COG:H||GO:0004108,GO:0046912,GO:0006101|EC:2.3.3.1|PF00285|IPR010109,IPR036969,IPR016143,IPR016142,IPR002020,IPR019810 (complex (high (translocase

[vdemichev]

Options:

• Reformat FASTA to match the UniProt format using some R or Python package that handles FASTAs
• Analyse as is, set protein inference to 'isoforms' in DIA-NN, annotate its main report with gene names using some R or Python package