Last modified on 11 October 2011.

Highlights / Data

Sections on This Page:

  • Primary Alignments: our largest and most complete collections of well-aligned sequences.
  • Seed Alignments: derived from primary alignments, smaller alignments that have been highly refined; useful starting points for new alignments.
  • Specialized Alignments: derived from primary alignments, phylogenetic subsets of the major alignments.
  • Pre-Primary Alignments: precursors to primary alignments; more sequences, but parts of the alignment are unrefined (particularly ends of sequences and variable regions).
  • rCAD Datasets: Ribosomal RNA datasets, including structure models spanning the Tree of Life, formatted for import into the rCAD database.
  • Alignments Used in Specific Analyses: alignments that have appeared in Gutell Lab publications.

Additional Information:

Primary Alignments:

Table 1: Ribosomal RNA Alignments

Alignment (Abbreviation) 5S rRNA 16S rRNA 23S rRNA
AE2 | GB | alnFA | rawFASeqs AE2 | GB | alnFA | rawFASeqs AE2 | GB | alnFA | rawFASeqs
Archaea (A) AE2 | GB | alnFA | rawFA147 AE2 | GB | alnFA | rawFA788 AE2 | GB | alnFA | rawFA226
Bacteria (B) AE2 | GB | alnFA | rawFA2,637 AE2 | GB | alnFA | rawFA35,998 AE2 | GB | alnFA | rawFA5,947
Chloroplast (C) AE2 | GB | alnFA | rawFA199 AE2 | GB | alnFA | rawFA404 AE2 | GB | alnFA | rawFA442
Eukaryota (E) AE2 | GB | alnFA | rawFA2,845 AE2 | GB | alnFA | rawFA1,937 AE2 | GB | alnFA | rawFA115
Mitochondria (M) AE2 | GB | alnFA | rawFA49 AE2 | GB | alnFA | rawFA899 AE2 | GB | alnFA | rawFA285
Three Phylogenetic Domains (3) AE2 | GB | alnFA | rawFA5,624 AE2 | GB | alnFA | rawFA5,591 AE2 | GB | alnFA | rawFA585
Three Phylogenetic Domains/Two Organelles (T) AE2 | GB | alnFA | rawFA5,868 AE2 | GB | alnFA | rawFA6,389 AE2 | GB | alnFA | rawFA922

Table 2: Intron RNA Alignments

Alignment (Abbreviation) Intron RNA
AE2 | GB | alnFA | rawFASeqs
Group IA Introns AE2 | GB | alnFA | rawFA109
Group IB Introns AE2 | GB | alnFA | rawFA201
Group IC1 Introns AE2 | GB | alnFA | rawFA818
Group IC2 Introns AE2 | GB | alnFA | rawFA31
Group IC3 Introns AE2 | GB | alnFA | rawFA984
Group ID Introns AE2 | GB | alnFA | rawFA21
Group IE Introns AE2 | GB | alnFA | rawFA248
Group IIA Introns AE2 | GB | alnFA | rawFA174
Group IIB Introns AE2 | GB | alnFA | rawFA607

Table 3: Transfer RNA Alignments

Alignment (Abbreviation) [Type] Non-Mitochondrial tRNA Mitochondrial tRNA
AE2 | GB | alnFA | rawFASeqs AE2 | GB | alnFA | rawFASeqs
Alanine (A) [Type 1] AE2 | GB | alnFA | rawFA4,705 N/A
Cysteine (C) [Type 1] AE2 | GB | alnFA | rawFA890 N/A
Aspartate (D) [Type 1] AE2 | GB | alnFA | rawFA1,455 N/A
Glutamate (E) [Type 1] AE2 | GB | alnFA | rawFA1,935 N/A
Phenylalanine (F) [Type 1] AE2 | GB | alnFA | rawFA7,723 N/A
Glycine (G) [Type 1] AE2 | GB | alnFA | rawFA2,713 N/A
Histidine (H) [Type 1] AE2 | GB | alnFA | rawFA1,802 N/A
Isoleucine (I) [Type 1] AE2 | GB | alnFA | rawFA4,774 N/A
Lysine (K) [Type 1] AE2 | GB | alnFA | rawFA1,935 N/A
Methionine (M) [Type 1] AE2 | GB | alnFA | rawFA1,886 N/A
Asparagine (N) [Type 1] AE2 | GB | alnFA | rawFA1,261 N/A
Proline (P) [Type 1] AE2 | GB | alnFA | rawFA1,451 N/A
Glutamine (Q) [Type 1] AE2 | GB | alnFA | rawFA1,230 N/A
Tryptophan (W) [Type 1] AE2 | GB | alnFA | rawFA803 N/A
Tyrosine (Y1) [Type 1] AE2 | GB | alnFA | rawFA187 N/A

Seed Alignments:

Alignment (Abbreviation) 5S rRNA 16S rRNA 23S rRNA
AE2 | GB | alnFA | rawFASeqs AE2 | GB | alnFA | rawFASeqs AE2 | GB | alnFA | rawFASeqs
Archaea N/A AE2 | GB | alnFA | rawFA132 AE2 | GB | alnFA | rawFA144
Bacteria N/A AE2 | GB | alnFA | rawFA1,266 AE2 | GB | alnFA | rawFA1,681

Specialized Alignments:

Table 1: Ribosomal RNA Alignments

Alignment (Abbreviation) 5S rRNA 16S rRNA 23S rRNA
AE2 | GB | alnFA | rawFASeqs AE2 | GB | alnFA | rawFASeqs AE2 | GB | alnFA | rawFASeqs
Archaea      
Crenarchaeota N/A AE2 | GB | alnFA | rawFA105 N/A
Euryarchaeota N/A AE2 | GB | alnFA | rawFA567 N/A
Bacteria      
Actinobacteria AE2 | GB | alnFA | rawFA55 AE2 | GB | alnFA | rawFA4,510 N/A
Aquificae N/A AE2 | GB | alnFA | rawFA308 N/A
Bacteroidetes/Chlorobi group N/A AE2 | GB | alnFA | rawFA280 N/A
Chlamydiae/Verrucomicrobia group N/A AE2 | GB | alnFA | rawFA64 N/A
Chloroflexi N/A AE2 | GB | alnFA | rawFA11 N/A
Cyanobacteria N/A AE2 | GB | alnFA | rawFA388 N/A
Deinococcus-Thermus N/A AE2 | GB | alnFA | rawFA124 N/A
Fibrobacteres/Acidobacteria group N/A AE2 | GB | alnFA | rawFA23 N/A
Firmicutes AE2 | GB | alnFA | rawFA125 AE2 | GB | alnFA | rawFA6,556 N/A
Bacillus/Clostridium group AE2 | GB | alnFA | rawFA71 N/A N/A
Bacilli N/A AE2 | GB | alnFA | rawFA5,363 N/A
Clostridia N/A AE2 | GB | alnFA | rawFA540 N/A
Mollicutes N/A AE2 | GB | alnFA | rawFA496 N/A
Fusobacteria N/A AE2 | GB | alnFA | rawFA50 N/A
Nitrospirae N/A AE2 | GB | alnFA | rawFA22 N/A
Planctomycetes N/A AE2 | GB | alnFA | rawFA34 N/A
Proteobacteria AE2 | GB | alnFA | rawFA165 AE2 | GB | alnFA | rawFA11,200 AE2 | GB | alnFA | rawFA164
Alphaproteobacteria AE2 | GB | alnFA | rawFA50 AE2 | GB | alnFA | rawFA3,172 N/A
Betaproteobacteria AE2 | GB | alnFA | rawFA28 AE2 | GB | alnFA | rawFA3,254 N/A
Delta/Epsilon subdivisions N/A AE2 | GB | alnFA | rawFA707 N/A
Gammaproteobacteria AE2 | GB | alnFA | rawFA82 AE2 | GB | alnFA | rawFA3,928 AE2 | GB | alnFA | rawFA78
Spirochaetes N/A AE2 | GB | alnFA | rawFA666 N/A
Thermotogae N/A AE2 | GB | alnFA | rawFA76 N/A
Eukaryota      
Acanthamoebidae N/A AE2 | GB | alnFA | rawFA132 N/A
Coccidia N/A AE2 | GB | alnFA | rawFA125 N/A
Entamoebidae N/A AE2 | GB | alnFA | rawFA17 N/A
Giardiinae N/A AE2 | GB | alnFA | rawFA18 N/A
Haemosporida N/A AE2 | GB | alnFA | rawFA24 N/A
Haplosporida N/A AE2 | GB | alnFA | rawFA10 N/A
Heterolobosea N/A AE2 | GB | alnFA | rawFA29 N/A
Litostomatea N/A AE2 | GB | alnFA | rawFA28 N/A
Lobosea N/A AE2 | GB | alnFA | rawFA58 N/A
Parabasalidea N/A AE2 | GB | alnFA | rawFA68 N/A
Perkinsea N/A AE2 | GB | alnFA | rawFA10 N/A
Piroplasmida N/A AE2 | GB | alnFA | rawFA106 N/A
stramenopiles N/A N/A N/A
Bacillariophyta N/A AE2 | GB | alnFA | rawFA181 N/A
Blastocystis N/A AE2 | GB | alnFA | rawFA49 N/A
Oomycetes N/A AE2 | GB | alnFA | rawFA19 N/A
Trypanosomatidae N/A AE2 | GB | alnFA | rawFA174 N/A
Viridiplantae N/A N/A N/A
Streptophyta N/A AE2 | GB | alnFA | rawFA2,023 N/A

Pre-Primary Alignments:

Table 1: Ribosomal RNA Alignments

Additional subalignments (marked "FUTURE") and filetypes (AE2, GB, rawFASTA) will be available once the CRW Site migrates to its new server (see the front page for details).
Alignment (Abbreviation) 5S rRNA 16S rRNA 23S rRNA
AE2 | GB | alnFA | rawFASeqs AE2 | GB | alnFA | rawFASeqs AE2 | GB | alnFA | rawFASeqs
Bacteria N/A AE2 | GB | alnFA | rawFA172,373 N/A
Actinobacteria N/A FUTURE 18,013 N/A
Aquificae N/A FUTURE 397 N/A
Bacteroidetes/Chlorobi group N/A FUTURE 7,396 N/A
Caldiserica N/A FUTURE 11 N/A
Chlamydiae/Verrucomicrobia group N/A FUTURE 135 N/A
Chloroflexi N/A FUTURE 32 N/A
Cyanobacteria N/A AE2 | GB | alnFA | rawFA2,770 N/A
Deinococcus-Thermus N/A FUTURE 239 N/A
Dictyoglomi N/A FUTURE 3 N/A
Fibrobacteres/Acidobacteria group N/A FUTURE 68 N/A
Firmicutes N/A AE2 | GB | alnFA | rawFA33,658 N/A
Bacilli N/A FUTURE 28,385 N/A
Clostridia N/A FUTURE 4,007 N/A
Fusobacteria N/A FUTURE 362 N/A
Nitrospirae N/A FUTURE 161 N/A
Planctomycetes N/A FUTURE 418 N/A
Proteobacteria N/A FUTURE 85,665 N/A
Alphaproteobacteria N/A FUTURE 20,740 N/A
Betaproteobacteria N/A FUTURE 16,035 N/A
Delta/Epsilon subdivisions N/A FUTURE 4,492 N/A
Deltaproteobacteria N/A FUTURE 2,739 N/A
Epsilonproteobacteria N/A FUTURE 1,754 N/A
Gammaproteobacteria N/A AE2 | GB | alnFA | rawFA44,118 N/A
Spirochaetes N/A AE2 | GB | alnFA | rawFA1,890 N/A
Synergistetes N/A FUTURE 1 N/A
Tenericutes N/A AE2 | GB | alnFA | rawFA1,459 N/A
Thermodesulfobacteria N/A FUTURE 12 N/A
Thermotogae N/A FUTURE 215 N/A
unclassified Bacteria N/A FUTURE 2,057 N/A
environmental samples N/A FUTURE 68,123 N/A

rCAD Data Sets in CRW Format:

Alignment (Abbreviation) 5S rRNA 16S rRNA 23S rRNA
CRWSeqsStr CRWSeqsStr CRWSeqsStr
Three Phylogenetic Domains CRW 5355 2908 CRW 5762 2361 CRW 670 0

Alignments Used in Specific Analyses:

Reference Description Alignments
4A (2003). rRNA Spliceosomal Introns SSU rRNA: All Fungi (1434 sequences) AE2 | GB
SSU rRNA: Spliceosomal Intron-Lacking Fungi (1361 sequences) AE2 | GB
SSU rRNA: Spliceosomal Intron-Containing Fungi (73 sequences) AE2 | GB
LSU rRNA: All Fungi (880 sequences) AE2 | GB
LSU rRNA: Spliceosomal Intron-Lacking Fungi (840 sequences) AE2 | GB
LSU rRNA: Spliceosomal Intron-Containing Fungi (40 sequences) AE2 | GB
4B (2001). AA.AG@helix.ends SSU rRNA (Bacteria) AE2 | GB
SSU rRNA (Archaea) AE2 | GB
SSU rRNA (Eucarya (Nuclear)) AE2 | GB
SSU rRNA (Eucarya (Chloroplast)) AE2 | GB
SSU rRNA (Eucarya (Mitochondria)) AE2 | GB
LSU rRNA (Bacteria) AE2 | GB
LSU rRNA (Archaea) AE2 | GB
LSU rRNA (Eucarya (Nuclear)) AE2 | GB
LSU rRNA (Eucarya (Chloroplast)) AE2 | GB
LSU rRNA (Eucarya (Mitochondria)) AE2 | GB
4D (2000). Mollusk Mitochondria Eleven mollusk sequences, plus Drosophila and Escherichia as reference points. GB
4D (2001). Polytoma Leucoplasts 16S rRNA sequence alignment (five chloroplasts, E. coli, and a chloroplast consensus). GB | PHYLIP
4D (2003). ITS (Asteraceae) Alignment of ITS1, 5.8S rRNA, and ITS2. AE2 | GB | Nexus
4D (2006). Diatom Shape Alignment of 181 diatom taxa, plus E. coli and outgroup sequences. AE2 | GB | Nexus
4E (2001). Red Algae / Brown Algae 604 SSU rRNA sequences. AE2 | GB
452 Group I intron sequences. AE2 | GB
4E (2005). Fungi / Red Algae Alignment of fifty Group IE Intron sequences; Nexus file contains analyzed columns only. AE2 | GB | Nexus