Question: Hi everybody,

I have to convert the genebank file of my virus genome to a gtf file for the aligment of my reads with STAR. I tried different tools, which I found by google search, but I doesn't work unfortunately.

I tried to do it with a perl script I found, called genbank2gtf_mRNA.pl from genebank2gtf and I tried a python script, called gb2gtf.py from lpryszcz, but when using the perl script with a custom chromosome file, I get an empty gtf file and when I tried to use the python script, I get the error: "command didn't found".

Can someone maybe recommend a converter tool or platform which I could use?

And; the genebank file contains splice site annotation from genious, does the conversion translate these coordinates?

Any help is greatfully appreciated :)

Edited: data exemple and tools, I struggled with

My gb data looks something like that:

> FEATURES Location/Qualifiers
> repeat_region 552..634
> /vntifkey="34"
> /label=U5
> CDS 5830..8414
> /vntifkey="4"
> /label=TAT
> /note="HIV-1 tat protein"
> splicing_signal 5934..5935
> /vntifkey="38"
> /label=SA4c
> splicing_signal 5952..5953
> /vntifkey="38"
> /label=SA4a
> splicing_signal 5958..5959
> /vntifkey="38"
> /label=SA4b
> CDS 8787..9407
> /vntifkey="4"
> /label=NEF
> /note="HIV-1 nef protein"
> splicing_signal 5775..5776
> /vntifkey="38"
> /label=SA3
> splicing_signal 6045..6046
> /vntifkey="38"
> /label=SD4
> CDS 5969..8643
> /vntifkey="4"
> /label=REV
> /note="HIV-1 rev protein"
> splicing_signal 5974..5975
> /vntifkey="38"
> /label=SA5
> CDS 2085..5096
> /vntifkey="4"
> /label=POL
> /note="HIV-1 pol polyprotein; (NH2-terminus uncertain)"
> CDS 5041..5619
> /vntifkey="4"
> /label=VIF
> /note="HIV-1 vif protein"
> CDS 5559..5849
> /vntifkey="4"
> /label=VPR
> /note="HIV-1 vpr protein"
> repeat_region 9529..9626
> /vntifkey="34"
> /label=R
> /note="HIV-1 R repeat 3' copy"
> CDS 6061..6306
> /vntifkey="4"
> /label=VPU
> /note="HIV-1 vpu protein"
> CDS 6221..8785
> /vntifkey="4"
> /label=ENV
> /note="HIV-1 envelope polyprotein"
> splicing_signal 6602..6603
> /vntifkey="38"
> /label=(SA6)
> splicing_signal 6720..6721
> /vntifkey="38"
> /label=(SD5)
> /note="Mutation von GT in anderen Isolaten zu AT"
> splicing_signal 8367..8368
> /vntifkey="38"
> /label=SA7
> LTR 1..634
> /vntifkey="19"
> /label=5'_LTR
> /note="HIV-1 5' LTR"
> repeat_region 454..551
> /vntifkey="34"
> /label=R
> /note="HIV-1 R repeat 5' copy"
> intron 744..5776
> /vntifkey="15"
> /label=TAT/REV/NEF_I
> /note="HIV-1 tat, rev, nef mRNA intron 1"
> misc_feature 5743..5744
> /vntifkey="21"
> /label=JNCTN_NY5/LAV
> /note="HIV-1 isolate NY5 DNA end/HIV-1 isolate LAV DNA start"
> intron 6045..8368
> /vntifkey="15"
> /label=TAT_II
> /note="HIV-1 tat cds intron 2"
> CDS 790..2292
> /vntifkey="4"
> /label=GAG
> /note="HIV-1 gag polyprotein"
> insertion_seq 1186..1186
> /vntifkey="14"
> /label=p17/p24
> splicing_signal 4963..4964
> /vntifkey="38"
> /label=SD2
> splicing_signal 744..745
> /vntifkey="38"
> /label=SD1
> splicing_signal 4911..4912
> /vntifkey="38"
> /label=SA1
> splicing_signal 5464..5465
> /vntifkey="38"
> /label=SD3
> polyA_signal 9602..9607
> /vntifkey="25"
> /label=POLY_A
> /note="HIV-1 mRNA polyadenlyation signal"
> splicing_signal 5388..5389
> /vntifkey="38"
> /label=SA2
> intron 6045..8368
> /vntifkey="15"
> /label=REV_II
> /note="HIV-1 rev cds intron 2"
> intron 6045..8368
> /vntifkey="15"
> /label=TAT/REV/NEF_II
> /note="HIV-1 tat, rev, nef mRNA intron 2"
> LTR 9076..9709
> /vntifkey="19"
> /label=3'_LTR
> /note="HIV-1 3' LTR"
> misc_feature 5059..5060
> /vntifkey="21"
> /label=SD2b
> splicing_signal 8335..8336
> /vntifkey="38"
> /label=SA7a
> splicing_signal 8440..8441
> /vntifkey="38"
> /label=SA7b
> splicing_signal 4541..4542
> /vntifkey="38"
> /label=SA1a
> splicing_signal 4722..4723
> /vntifkey="38"
> /label=SD1a BASE COUNT 3423 a 1756 c 2364 g 2166 t ORIGIN
> 1 tggaa....

Answer: I think you can use GFF file with STAR aligner.

https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf

> 2.2.3 Annotations in GFF format.

>In addition to the aforementioned options, for GFF3 formatted annotations you need to use
> --sjdbGTFtagExonParentTranscript Parent. In general, for --sjdbGTFfile files STAR only processes lines which have --sjdbGTFfeatureExon (=exon
> by default) in the 3rd field (column). The exons are assigned to the
> transcripts using parent-child relationship defined by the
> --sjdbGTFtagExonParentTranscript (=transcript id by default) GTF/GFF attribute.

If you would like to convert GFF3 to GTF then you can use gffread.
Please look at this post for further details: https://www.biostars.org/p/45791/