Hi Joao,

How were your sequences produced?

Sequencing involves the use of adapters that are not 16S. If your sequences weren't cleaned up properly, they could still contain the adapters. It is also recommended to trim off the primers.

I hope this helps even if I am not answering your question specifically.

Marine

I used Barnap by T Seemann (http://www.vicbioinformatics.com/) to check my NGS sequences for 16S sequences. It may help you identify the correct start and end points. 

Hi, mothur is a good pipeline for trimming and chimera check, e.g. There are good tutorials, a wiki and it is open source.  It is also very userfriendly. 

QIIME is another pipeline, you could use but it is a little bit more complicated if you are beginner in bioinformatics. But it might be very usefull and can handle bigger datasets than mothur.

http://www.mothur.org/

http://www.mothur.org/wiki/Trim.seqs

http://www.mothur.org/wiki/Chimera.uchime

http://qiime.org/

You must have the trace files. one fwd and reverse .abi files.

You may assemble .abi files using DNA Baser . You can download from here

http://www.dnabaser.com/

after assembly you will get the contigs in FASTA format.

input the FASTA sequence in Blast

from here https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch

select the database16S RNA ribosomal for bacteria and archae

You can identify your organism by interpreting the blast result.

Then you can proceed for a bankit submission to NCBI.

Hope this may help you!!

Thanks for all the help and ideas.

I use mothur and QIIME for metagenome analyses, but for this case (some 16S rRNA sequences) just I will check the analysis report obtained for each sequence after the sequencing step. Of course in addition to check the sequences by blast.

Thank you again for your help