Ribosomal Database Project Tips

Tips for using the RDP-II site

  File Formats

  Several of the RDP analysis tools allow one to upload files from the user's computer. Supported formats include: IG/Stanford, Olsen, GenBank/GB, Phylip3.2, NBRF, Phylip, EMBL, Plain/Raw, GCG, PIR/CODATA, DNAStrider, MSF, Fitch, ASN.1, Pearson/Fasta, PAUP/NEXUS, and Zuker. Phylip files containing multiple sequences may be interleaved or noninterleaved. PAUP/NEXUS files with multiple sequences do not always work.

To include the original data in the output from the RDP analysis, check the "Display converted input" button.

  Sample formats:

EMBL format

ID   UserSeq
DE   UserSeq, 430 bases, 919 checksum.
SQ             430 BP
     GTCTACAACC CAGCAGAACA CCGCTGCGGC CATGGCCCAT TTCTACCAGA
     AGAAGGTGTT TATCCACGGC TGCGATCCCA AAGCGGATTC CACCCGGCTT
     ATTCTAGGGG GCAAACCCCA GGAAACCCTG ATGGATGTGC TGCGCCAGGA
     GGGGGCGGAA AAGGTTACCA ATGACAAGGT TATCAAAACC GGGTTTCTGG
     ATATTCGTTG TGTAGAATCC GGGGGACCCG AGCCGGGGGT AGGCTGCGCT
     GGGCGGGGGG TAATTACCGC CATCGACCTG ATGGAAAACA ACGGCGCCTA
     TACGGAGGAC CTGGACTTTG TGTTCTTCGA TGTCCTGGGG GACGTTGTCT
     GCGGAGGCTT CGCCATGCCT ATCCGGGACG GCAAAGCCCA GGAGGTTTAT
     ATCGTAGCCT CCGGGGAAAT GATGGCCATC
//

fasta/Pearson format

>UserSeq, 430 bases, 919 checksum.
GTCTACAACCCAGCAGAACACCGCTGCGGCCATGGCCCATTTCTACCAGA
AGAAGGTGTTTATCCACGGCTGCGATCCCAAAGCGGATTCCACCCGGCTT
ATTCTAGGGGGCAAACCCCAGGAAACCCTGATGGATGTGCTGCGCCAGGA
GGGGGCGGAAAAGGTTACCAATGACAAGGTTATCAAAACCGGGTTTCTGG
ATATTCGTTGTGTAGAATCCGGGGGACCCGAGCCGGGGGTAGGCTGCGCT
GGGCGGGGGGTAATTACCGCCATCGACCTGATGGAAAACAACGGCGCCTA
TACGGAGGACCTGGACTTTGTGTTCTTCGATGTCCTGGGGGACGTTGTCT
GCGGAGGCTTCGCCATGCCTATCCGGGACGGCAAAGCCCAGGAGGTTTAT
ATCGTAGCCTCCGGGGAAATGATGGCCATC

GCG_text format

UserSeq
    UserSeq  Length: 430  Fri, Jan 29, 1999  4:10 AM  Check: 919  ..
       1  GTCTACAACC CAGCAGAACA CCGCTGCGGC CATGGCCCAT TTCTACCAGA
      51  AGAAGGTGTT TATCCACGGC TGCGATCCCA AAGCGGATTC CACCCGGCTT
     101  ATTCTAGGGG GCAAACCCCA GGAAACCCTG ATGGATGTGC TGCGCCAGGA
     151  GGGGGCGGAA AAGGTTACCA ATGACAAGGT TATCAAAACC GGGTTTCTGG
     201  ATATTCGTTG TGTAGAATCC GGGGGACCCG AGCCGGGGGT AGGCTGCGCT
     251  GGGCGGGGGG TAATTACCGC CATCGACCTG ATGGAAAACA ACGGCGCCTA
     301  TACGGAGGAC CTGGACTTTG TGTTCTTCGA TGTCCTGGGG GACGTTGTCT
     351  GCGGAGGCTT CGCCATGCCT ATCCGGGACG GCAAAGCCCA GGAGGTTTAT
     401  ATCGTAGCCT CCGGGGAAAT GATGGCCATC

GenBank format

LOCUS       UserSeq       430 bp
DEFINITION  UserSeq, 430 bases, 919 checksum.
ORIGIN      
       1  GTCTACAACC CAGCAGAACA CCGCTGCGGC CATGGCCCAT TTCTACCAGA
      51  AGAAGGTGTT TATCCACGGC TGCGATCCCA AAGCGGATTC CACCCGGCTT
     101  ATTCTAGGGG GCAAACCCCA GGAAACCCTG ATGGATGTGC TGCGCCAGGA
     151  GGGGGCGGAA AAGGTTACCA ATGACAAGGT TATCAAAACC GGGTTTCTGG
     201  ATATTCGTTG TGTAGAATCC GGGGGACCCG AGCCGGGGGT AGGCTGCGCT
     251  GGGCGGGGGG TAATTACCGC CATCGACCTG ATGGAAAACA ACGGCGCCTA
     301  TACGGAGGAC CTGGACTTTG TGTTCTTCGA TGTCCTGGGG GACGTTGTCT
     351  GCGGAGGCTT CGCCATGCCT ATCCGGGACG GCAAAGCCCA GGAGGTTTAT
     401  ATCGTAGCCT CCGGGGAAAT GATGGCCATC
//

IG format

;UserSeq, 430 bases, 919 checksum.
UserSeq
GTCTACAACCCAGCAGAACACCGCTGCGGCCATGGCCCATTTCTACCAGA
AGAAGGTGTTTATCCACGGCTGCGATCCCAAAGCGGATTCCACCCGGCTT
ATTCTAGGGGGCAAACCCCAGGAAACCCTGATGGATGTGCTGCGCCAGGA
GGGGGCGGAAAAGGTTACCAATGACAAGGTTATCAAAACCGGGTTTCTGG
ATATTCGTTGTGTAGAATCCGGGGGACCCGAGCCGGGGGTAGGCTGCGCT
GGGCGGGGGGTAATTACCGCCATCGACCTGATGGAAAACAACGGCGCCTA
TACGGAGGACCTGGACTTTGTGTTCTTCGATGTCCTGGGGGACGTTGTCT
GCGGAGGCTTCGCCATGCCTATCCGGGACGGCAAAGCCCAGGAGGTTTAT
ATCGTAGCCTCCGGGGAAATGATGGCCATC1

NBRF format

>DL;UserSeq
UserSeq, 430 bases, 919 checksum.
 GTCTACAACC CAGCAGAACA CCGCTGCGGC CATGGCCCAT TTCTACCAGA
 AGAAGGTGTT TATCCACGGC TGCGATCCCA AAGCGGATTC CACCCGGCTT
 ATTCTAGGGG GCAAACCCCA GGAAACCCTG ATGGATGTGC TGCGCCAGGA
 GGGGGCGGAA AAGGTTACCA ATGACAAGGT TATCAAAACC GGGTTTCTGG
 ATATTCGTTG TGTAGAATCC GGGGGACCCG AGCCGGGGGT AGGCTGCGCT
 GGGCGGGGGG TAATTACCGC CATCGACCTG ATGGAAAACA ACGGCGCCTA
 TACGGAGGAC CTGGACTTTG TGTTCTTCGA TGTCCTGGGG GACGTTGTCT
 GCGGAGGCTT CGCCATGCCT ATCCGGGACG GCAAAGCCCA GGAGGTTTAT
 ATCGTAGCCT CCGGGGAAAT GATGGCCATC*

NEXUS (PAUP) format

#NEXUS
[!This data assembled using Sequencher™, from Gene Codes Corporation.]
begin data;
   dimensions ntax=1 nchar=430;
   format datatype=dna gap=: interleave;
   matrix
UserSeq_430 GTC TAC AAC CCA GCA GAA CAC CGC TGC GGC CAT GGC CCA TTT CTA CCA
UserSeq_430 GAA GAA GGT GTT TAT CCA CGG CTG CGA TCC CAA AGC GGA TTC CAC CCG
UserSeq_430 GCT TAT TCT AGG GGG CAA ACC CCA GGA AAC CCT GAT GGA TGT GCT GCG
UserSeq_430 CCA GGA GGG GGC GGA AAA GGT TAC CAA TGA CAA GGT TAT CAA AAC CGG
UserSeq_430 GTT TCT GGA TAT TCG TTG TGT AGA ATC CGG GGG ACC CGA GCC GGG GGT
UserSeq_430 AGG CTG CGC TGG GCG GGG GGT AAT TAC CGC CAT CGA CCT GAT GGA AAA
UserSeq_430 CAA CGG CGC CTA TAC GGA GGA CCT GGA CTT TGT GTT CTT CGA TGT CCT
UserSeq_430 GGG GGA CGT TGT CTG CGG AGG CTT CGC CAT GCC TAT CCG GGA CGG CAA
UserSeq_430 AGC CCA GGA GGT TTA TAT CGT AGC CTC CGG GGA AAT GAT GGC CAT C
;
endblock;

Raw_text (ASCII) format

GTCTACAACCCAGCAGAACACCGCTGCGGCCATGGCCCATTTCTACCAGA
AGAAGGTGTTTATCCACGGCTGCGATCCCAAAGCGGATTCCACCCGGCTT
ATTCTAGGGGGCAAACCCCAGGAAACCCTGATGGATGTGCTGCGCCAGGA
GGGGGCGGAAAAGGTTACCAATGACAAGGTTATCAAAACCGGGTTTCTGG
ATATTCGTTGTGTAGAATCCGGGGGACCCGAGCCGGGGGTAGGCTGCGCT
GGGCGGGGGGTAATTACCGCCATCGACCTGATGGAAAACAACGGCGCCTA
TACGGAGGACCTGGACTTTGTGTTCTTCGATGTCCTGGGGGACGTTGTCT
GCGGAGGCTTCGCCATGCCTATCCGGGACGGCAAAGCCCAGGAGGTTTAT
ATCGTAGCCTCCGGGGAAATGATGGCCATC

Upload and download limitations

In order to avoid overtaxing the server, we sometimes ask that the number of sequences uploaded be limited to less than fifty. Loading more than fifty sequences will cause an error message to appear.

When downloading the results of an analysis for viewing in Netscape, the application will freeze if the downloaded file is larger than about 2.4 MB. This usually only occurs with Probe Match when checking a probe that hits many sequences.

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