Supplementary Material

This web site supplements my article, "Faster genome annotation of non-coding RNA families without loss of accuracy" with the raw results of the scans, containing the new ncRNA  homologs discovered by the more sensitive technique.  If you use this data in your own research, please cite my article:

Z. Weinberg and W.L. Ruzzo (2004) "Faster genome annotation of non-coding RNA families without loss of accuracy", Proc. Eighth Annual Inter. Conf. on Computational Molecular Biology (RECOMB), p. 243-251.
Preprint: in Postscript, in Adobe Acrobat .pdf

The software that implemented the techniques in this paper is avilable for download here

The following table has a link to the current version of the Rfam Database for each ncRNA family that was scanned for this paper.  It then gives the raw results (.cmzasha), and a comma-separated file (.csv) that is more convenient to look at, and notates which family members were already in Rfam 5.0, and which were new.

Instructions:

• About the .csv format
• About the .cmzasha format

In the following table, the first column is the Rfam accession number (see Rfam database Web site).  Next is a link to the given family in the current version of Rfam (which at some point in the future will be later than the Rfam 5.0 version that was used for my paper).  Next is a brief description of the family; the Rfam link has a paragraph on each family, and a couple of useful references.  The # known is the number of family members as reported in Rfam 5.0.  # new is the number of additional members found with the more sensitive technique (using the version of RFAMSEQ appropraite to Rfam 5.0).  Next is the .cmzasha file, which is the raw output of my program, and the .csv file, which is the result of processing the raw output slightly.

(Download all results files from the below table at once: tar & gzip archive)

Rfam Id	link to Rfam	name	# known	# new	.cmzasha (raw scan)	.csv (comma-separated file)
RF00008 (Rfam 4.0)	N/A	Hammerhead ribozyme	313	278	file	N/A
RF00008	link	Hammerhead ribozyme	251	13	file	file
RF00012	link	U3 snRNA	129	0	file	file
RF00015	link	U4 snRNA	283	7	file	file
RF00019	link	Y RNA	1107	0	file	file
RF00020	link	U5 snRNA	199	1	file	file
RF00024	link	vertebrate telomerase	51	0	file	file
RF00025	link	ciliate telomerase	17	0	file	file
RF00026	link	U6 snRNA	1462	2	file	file
RF00027	link	let-7 microRNA	30	0	file	file
RF00030	link	RNase MRP	39	0	file	file
RF00032	link	Histone 3' element	1004	102	file	file
RF00037	link	Iron response element	201	121	file	file
RF00043	link	Plasmid copy control	8	0	file	file
RF00050	link	RFN element	107	0	file	file
RF00052	link	lin-4 microRNA	14	0	file	file
RF00053	link	mir-7 microRNA	10	0	file	file
RF00054	link	U25 snoRNA	28	0	file	file
RF00055	link	snoRNA Z37	28	0	file	file
RF00066	link	U7 snRNA	312	1	file	file
RF00075	link	mir-166 microRNA	14	0	file	file
RF00093	link	U18 snoRNA	43	0	file	file
RF00095	link	Pyrococcus snoRNA	57	123	file	file
RF00103	link	mir-1 microRNA	13	0	file	file
RF00104	link	mir-10 microRNA	34	0	file	file
RF00151	link	U58 snoRNA	12	0	file	file
RF00162	link	S box	128	3	file	file
RF00163	link	Hammerhead ribozyme	167	26	file	file
RF00164	link	Coronavirus s2m	115	0	file	file
RF00165	link	Coronavirus 3' UTR pseudoknot	60	0	file	file
RF00167	link	Purine element	69	54	file	file
RF00169	link	eubacterial SRP	162	0	file	file
RF00170	link	Retron msr RNA	11	48	file	file
RF00173	link	hairpin ribozyme	5	0	file	file

About the .csv format

This file is a comma-separated file, which is intended to be viewed in Microsoft Excel, or a similar program.  Otherwise, it's a text file, so viewable in any text editor, although the files are very long, so it's going to be tough to read.  With a simple script (e.g. with Perl), you could convert it to other formats.

The columns in the .csv file are:

• (Probably not useful.)  The parameters used to run my scan program (with the caveat that commas are changed to semicolons to follow the .csv format), which will probably not be helpful to you.
• (Probably not useful.)  The CM file name used in the scan, which basically just says what the Rfam accession Id is.
• (Probably not useful.)  The name of the genome sequence file that the hit in.  This will be a file that's a part of the the EMBL nucleotide database, release 76 (since RFAMSEQ, the nucleotide database searched by Rfam for all families, is basically a subset of EMBL)
• (Probably not useful.)  sequence #: which sequence this is within the EMBL file in the previous column, starting with 0.
• The EMBL accession ID of the sequence in which the putative homolog was found.  This accession ID is for EMBL release 76 (which at some point in the future, will be an old version of EMBL)
• (Probably not useful.)  Whether or not the given EMBL accession ID is a part of Rfam 5.0 version RFAMSEQ.  Always 1 (yes).  This field was useful to me when I had done scans on an old version of RFAMSEQ; now it's not useful even to me, because it's always 1.
• A description of the EMBL sequence, generated from the EMBL format by the sp2fasta program (part of WU-BLAST), which converts EMBL-format sequence files into FASTA-format files.
• is reversed?  If 0, the homolog is on the forward strand; if 1, the homolog is on the reverse strand.
• An ordinal hit #, starting at 0.  i.e. simply numbers all the homologs.
• start nuc.  The first nucleotide in the sequence that is part of the putative homolog.  If the homolog is on the reverse strand, start nuc will be greater than end nuc.
• end nuc.  Last nucleotide of the homolog.
• score (bits).  The logarithmic score assigned to the homolog by the family-specific covariance model.  In general, higher scores are more likely to be true homologs.  (With weasel words: higher scores indicate sequences that are more similar to the training data for the family.)
• The Rfam-format homolog IDs for all family members (homologs) in Rfam 5.0 that have exactly the same nucleotide sequence.  The hit ID format is EMBL-accession/start-nuc,end-nuc.
• Hit ranges (start-nuc - end-nuc) of all Rfam 5.0 hits that are in the same EMBL sequence as the given homolog.
• "new hitness".  0 means the homolog is already in Rfam 5.0.  1 means that the homolog overlaps (with at least 1 nucleotide) something already in Rfam, which usually means that the more sensitive search technique may have found slightly more optimal nucleotide boundaries for the homolog, but that it's fundamentally a hit in Rfam 5.0.  2 means that the sequence was not in Rfam 5.0.
• Biggest overlap (in nucleotides) with a homolog already in Rfam 5.0.  An overlap of 0 generally means that the homolog is not in Rfam 5.0.  Overlaps <10 usually means is close to another homolog, but is novel, and >10 usually means it's already there.
• (Probably not useful.)  This hit in Rfam format.  Gives this homolog in Rfam homolog ID format.  I forget why I put this in.

About the .cmzasha format

The .cmzasha file is the raw output of our software.  The information in it is essentially redundant with the .csv file.  Additional information is:

• the .cmzasha file gives an alignment of each putative homolog to the family's covariance model in the format of the Infernal software package used by Rfam.
• The end of the .cmzasha gives the filtering fractions for the profile HMM rigorous filter(s) used.  Note that, in contrast to the formalism of the paper, the filtering fraction in the .cmzasha file is a fraction of the output of the previous filter (or original database, if no previous filter), where the paper had the filtering fraction as always relative to the original database.  This affects the cases where both compact- and expanded-type HMMs were used in serial.
• The end of the .cmzasha also gives the CPU user time in seconds taken for the scan.