SeqMatch

Add a SeqMatch Database

SeqMatch preceded the RDP Classifier for as a means of classifying 16S rRNA gene sequences. It uses a kmer approach to finding the closest matches in a database.  Here I provide instructions for adding two SeqMatch databases to RDPTools.

Click on this link to download the archive file SeqMatch_DBs.zip. If you installed RDPTools using the Docker image, place the file in the folder you mapped to the container (see creating-the-container in my GitBook instructions for installing RDPTools from a Docker image) and decompress it. Otherwise place it in your home directory or wherever you wish. Decompressing the file generates the directory SeqMatch_DBs with the following files:

SeqMatch_DBs
     release11_4_type_descriptions.txt
     release11_4_bac_isolate_descriptions.txt
     isolate_trainee_files
          release11_4_bac_isolates_1.trainee
          release11_4_bac_isolates_2.trainee
          release11_4_bac_isolates_3.trainee
          release11_4_bac_isolates_4.trainee
          release11_4_bac_isolates_5trainee
          release11_4_bac_isolates_6.trainee
          release11_4_bac_isolates_7.trainee
          release11_4_bac_isolates_8.trainee

As you can see, there are two databases; one for type strains and another for bacterial isolates.

Using SeqMatch

Entering the following command¬† …

java -jar /usr/local/RDPTools/SequenceMatch.jar seqmatch

gives a help message for the seqmatch program:

To classify sequences in a fasta file with the type strains database (edit the paths as appropriate), use the command:

java -jar /usr/local/RDPTools/SequenceMatch.jar seqmatch \
    ~/SeqMatch_DBs/release11_4_types.trainee \
    query.fasta \
    --desc ~/SeqMatch_DBs/release11_4_type_descriptions.txt \
    --knn 20 \
    --sab 0.5 \
    --outFile query_classified.tsv

To classify sequences in a fasta file with the isolates database, use the command:

java -jar /usr/local/RDPTools/SequenceMatch.jar seqmatch \
    ~/SeqMatch_DBs/isolate_trainee_files \
    query.fasta \
    --desc ~/SeqMatch_DBs/release11_4_bac_isolate_descriptions.txt \
    --knn 20 \
    --sab 0.5 \
    --outFile query_classified.tsv