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DNA sequences trimming methods

Hello,

This is my situtation:

I have about 2000 DNA sequences to process, but I just want to work with the coding region of them. I have the coordinates of all CDSs (that I got with Prodigal) in a file with this format:

DEFINITION  seqnum=1;seqlen=8075;seqhdr="KU821590.1 Foot-and-mouth disease virus - type SAT 1 isolate SAT1/NAM01/2010, complete 
genome";version=Prodigal.v2.6.3;run_type=Single;model="Ab initio";gc_cont=53.37;transl_table=11;uses_sd=0
FEATURES             Location/Qualifiers
     CDS                      1026..8045

/note="ID=1_1;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.537;conf=99.99;score=1639.83;cscore=1612.89;sscore=26.93;rscore=-13.40;uscore=34.66;tscore=5.68;"

How could I extract the sequence file that corresponds to the coordinates into a FASTA file?

dna trimming sequence cds
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written by l.souza l.souza

You'll need to parse out the header and coordinate information from your file, then match to the headers in your fasta, and use the coordinates per header to cut each sequence.

Can you post a few more lines of your file from Prodigal?

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written by st.ph.n st.ph.n 
DEFINITION  seqnum=1;seqlen=8075;seqhdr="KU821590.1 Foot-and-mouth disease virus - type SAT 1 isolate SAT1/NAM01/2010, complete 
genome";version=Prodigal.v2.6.3;run_type=Single;model="Ab initio";gc_cont=53.37;transl_table=11;uses_sd=0
FEATURES             Location/Qualifiers
     CDS             1026..8045
                 /note="ID=1_1;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.537;conf=99.99;score=1639.83;cscore=1612.89;sscore=26.93;rscore=-13.40;uscore=34.66;tscore=5.68;"

DEFINITION  seqnum=2;seqlen=8010;seqhdr="KR108948.1 Foot-and-mouth disease virus - type SAT 1 isolate KNP/196/91/1 polyprotein gene, partial 
cds";version=Prodigal.v2.6.3;run_type=Single;model="Ab initio";gc_cont=53.37;transl_table=11;uses_sd=0
FEATURES             Location/Qualifiers
     CDS             1011..>8009
                 /note="ID=2_1;partial=01;start_type=ATG;rbs_motif=TTTA;rbs_spacer=14bp;gc_cont=0.537;conf=99.99;score=1624.62;cscore=1579.25;sscore=45.37;rscore=16.14;uscore=23.55;tscore=5.68;"

DEFINITION  seqnum=3;seqlen=8144;seqhdr="JF749860.1 Foot-and-mouth disease virus - type SAT 1 isolate KEN_004/2002, complete 
genome";version=Prodigal.v2.6.3;run_type=Single;model="Ab initio";gc_cont=53.37;transl_table=11;uses_sd=0
FEATURES             Location/Qualifiers
     CDS             1018..8037
                 /note="ID=3_1;partial=00;start_type=ATG;rbs_motif=AAA;rbs_spacer=14bp;gc_cont=0.540;conf=99.99;score=1468.42;cscore=1472.82;sscore=-4.40;rscore=0.64;uscore=-10.72;tscore=5.68;"

DEFINITION  seqnum=4;seqlen=8156;seqhdr="KM268899.1 Foot-and-mouth disease virus - type SAT 1 isolate TAN/22/2012, complete 
genome";version=Prodigal.v2.6.3;run_type=Single;model="Ab initio";gc_cont=53.37;transl_table=11;uses_sd=0
FEATURES             Location/Qualifiers
     CDS             1006..8025
                 /note="ID=4_1;partial=00;start_type=ATG;rbs_motif=TTTTA;rbs_spacer=14bp;gc_cont=0.537;conf=99.99;score=1462.32;cscore=1401.95;sscore=60.38;rscore=17.40;uscore=37.30;tscore=5.68;"

The file consists of repetitions like this...

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written by l.souza l.souza

Is this genbank format? You can convert it to bed (see some discussion here) and get the regions of interest with bedtools or bedops.

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written by h.mon h.mon

Not all of my sequences are genebank format!

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written by l.souza l.souza

What is the output format you chose for prodigal? Do you have a mix of formats?

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written by h.mon h.mon

Hello Lucas Souza!

We believe that this post does not fit the main topic of this site.

I could solve my problem calling ' -d ' in PRODIGAL parametres.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by l.souza l.souza

hi Lucas, you do not need to close the question, you may add your own answer and accept it. This would be better, as it would point a good solution to people with the same or similar questions.

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written by h.mon h.mon

Hi h.mom, I opened the question again. Thank you for the info!

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written by l.souza l.souza

1 answer

I could solve my problem calling ' -d ' in PRODIGAL parametres.

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written by l.souza l.souza

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