Supplementary Material

This web site supplements my article, "Exploiting Conserved Structure for Faster Annotation of Non-coding RNAs 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) "Exploiting Conserved Structure for Faster Annotation of Non-coding RNAs Without Loss of Accuracy", Bioinformatics, 20 (suppl. 1): i334-i340.  Presented at the 12th International Conference on Intelligent Systems for Molecular Biology (ISMB 2004) .

Download preprint: in Adobe Acrobat (pdf), in Postcript

Technical supplement

This supplementary paper describes additional technical information on the implementation:

Download supplement: in Adobe Acrobat (pdf), in Postscript

(Last updated October 6, 2004.)

Software download

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

Raw results of scans

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.  These results are for Rfam 5.0, which is no longer the current version.

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 appropriate 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)

Filter series used in scans

The following describes, for each family scanned, the series of filters used in that scan.  The selection of a filter series is now a fully automated process, as described in the technical supplement.  However, the scheme described in the ISMB paper is partially manual, and for some of the easier families, even more manual tasks were performed; for some families like RF00004, a better filter series could almost certainly be found.

For each family, a numbered list is given showing each filter in the order it is applied.  Each filter either begins with 'hmm', 'sub' (Sub-CM) or 'store-pair'.

If 'hmm' a profile HMM is used, and it's type (expanded or compact) is given.  (Note that the sub-CM and store-pair modifications are all applied on top of the expanded-type HMM).

After 'sub' the node at which the sub-CM is rooted is given, followed by the sub-CM-specific window length is given.  For example, for RF00001, "sub,40,60" is used, which is a Sub-CM rooted at node 40 using a window length of only 60 (even though the full ncRNA requires a window length of 180).  If multiple sub-CMs are used simultaneously in some filter, they are separated by front slashes ('/').

After 'store-pair', the list of modifications is given.  Each modification consists of a number followed by a string.  The number is the node that is to be modified.  The string specifies what information should be stored for the pair at that node.  The first letter says whether the left or right nucleotide is stored: 'l'=left, 'r'=right.  The remainder specifies a partition of the 5 symbols ACGU_ indicating what is stored.  The underscore ('_') represents the empty character (written as epsilon in the paper).  To specify the partition, the symbols are separated with a dash ('-').  For example, "store-pair,3,l-A_-CG-U,76,r-AG_-C-U" says that (1) node 3 is modified by remembering which of the following sets the left nucleotide fits into: {A,_} or {C,G} or {U}, and (2) node 76 is modified by remembering which of the following sets the right nucleotide fits into: {A,G,_} or {C} or {U}.

• RF00001
  1. hmm (expanded-type)
  2. store-pair,47,l-A-C-G-U-_,87,l-A-C-G-U-_
  3. store-pair,43,l-A-C-G-U-_,44,l-A-C-G-U-_,86,l-A-C-G-U-_,87,l-A-C-G-U-_
  4. sub,40,60
• RF00004
  1. hmm (expanded-type)
  2. store-pair,60,l-A-C-G-U-_,78,l-A-C-G-U-_,26,l-A-C-G-U-_,130,l-A-C-G-U-_,152,l-A-C-G-U-_
  3. store-pair,59,l-A-C-G-U-_,60,l-A-C-G-U-_,77,l-A-C-G-U-_,78,l-A-C-G-U-_,25,l-A-C-G-U-_,26,l-A-C-G-U-_,129,l-A-C-G-U-_,130,l-A-C-G-U-_,151,l-A-C-G-U-_,152,l-A-C-G-U-_
• RF00005
  1. store-pair,17,l-A_-CG-U,16,l-AG_-C-U,34,r-A_-CG-U,33,r-AG_-CU,32,r-AG_-CU,53,r-AGU-C-_,52,l-CGU-A_,51,r-AG_-CU
  2. store-pair,17,l-A_-CG-U,16,l-AG_-C-U,15,l-CU_-AG,34,r-C_-A-G-U,33,r-AG_-CU,32,r-AG_-CU,31,l-AG_-CU,53,r-AGU-C-_,52,l-CU_-A-G,51,r-AG_-CU,50,l-AG_-CU
  3. sub,30,40/sub,49,40
  4. sub,30,40/sub,49,40/sub,15,40
• RF00009
  1. store-pair,125,l-A-C-G-U-_,126,l-A-C-G-U-_,139,l-A-C-G-U-_,140,l-A-C-G-U-_,153,l-A-C-G-U-_,154,l-A-C-G-U-_,80,l-A-C-G-U-_,81,l-A-C-G-U-_,195,l-A-C-G-U-_,196,l-A-C-G-U-_
• RF00010
  1. hmm (expanded-type)
  2. store-pair,57,r-AG-U_-C,56,l-ACU_-G,72,r-AG-U_-C,71,r-AG_-CU,117,r-AG-CU-_,144,r-AGU-C-_,163,r-AGU-C-_,162,l-AG_-CU,203,r-ACGU-_,202,l-ACGU-_,229,r-A_-GU-C,228,l-AG_-CU,262,l-AU-C-G-_,261,r-CGU-A_
  3. store-pair,57,r-AG-U_-C,56,l-ACU_-G,55,r-AGU-C_,72,r-AG-U_-C,71,r-AG_-CU,70,l-CU_-AG,117,r-AG-CU-_,116,r-AG-CU-_,144,r-AGU-C-_,143,r-AU-C-G-_,163,r-AGU-C-_,162,l-A-C-G-U-_,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,229,r-A_-GU-C,228,l-AG-C-U-_,262,r-AC-GU-_,261,r-CGU-A_,260,r-AG-CU-_
  4. store-pair,57,r-AG-U_-C,56,l-ACU_-G,55,r-AGU-C_,54,l-AGU-C_,72,r-AU-C-G-_,71,r-AG_-CU,70,l-CU_-AG,69,r-ACU-G_,117,r-AG-CU-_,116,r-ACU-G_,115,l-ACU-G_,144,r-AGU-C-_,143,r-AU-C-G-_,140,r-AGU_-C,163,r-AGU-C-_,162,l-A-C-G-U-_,161,r-CU_-AG,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,196,l-ACGU-_,229,r-AG-C-U-_,228,l-AG-C-U-_,224,l-AG_-CU,262,r-AC-GU-_,261,l-AG-CU-_,259,r-AG-CU-_
  5. store-pair,57,r-AG-U_-C,56,l-ACU_-G,55,r-AGU-C_,54,l-AGU-C_,53,l-AGU_-C,72,r-AU-C-G-_,71,r-AG_-CU,70,l-CU_-AG,69,r-ACU-G_,67,l-AC_-GU,117,r-AG-CU-_,116,r-AG-CU-_,115,l-ACU-G_,113,r-ACU_-G,144,r-AGU-C-_,143,r-AU-C-G-_,140,r-AGU_-C,139,l-ACU_-G,163,r-AGU-C-_,162,l-AG-C-U-_,161,r-CU_-AG,157,l-CU_-AG,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,196,l-ACGU-_,178,l-ACGU-_,229,r-AG-C-U-_,228,l-AG-C-U-_,225,l-ACU-G_,224,l-AG_-CU,262,r-AC-GU-_,261,l-AG-CU-_,260,r-AG-CU-_,259,r-AG-CU-_
  6. store-pair,57,r-AG-U_-C,56,l-ACU_-G,55,r-A_-GU-C,54,l-AGU-C_,53,l-AGU_-C,72,r-AU-C-G-_,71,l-A_-CU-G,70,l-CU_-AG,69,r-ACU-G_,67,l-AC_-GU,117,r-AG-CU-_,116,r-AG-CU-_,115,l-AG-CU-_,113,r-ACU_-G,144,r-AGU-C-_,143,l-AG-CU-_,142,l-ACG-U_,140,r-AGU_-C,139,l-ACU_-G,163,r-AGU-C-_,162,l-A-C-G-U-_,161,r-CU_-AG,157,l-CU_-AG,156,r-ACU_-G,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,196,l-ACGU-_,177,l-AGU-C-_,229,r-AG-C-U-_,228,l-AG-C-U-_,225,r-AG-CU-_,224,l-AG_-CU,262,r-AC-GU-_,261,l-AG-CU-_,260,r-AG-CU-_,259,r-AG-CU-_,255,l-ACGU-_
  7. store-pair,57,r-AG-C-U-_,56,l-ACU_-G,55,r-A_-GU-C,54,r-CU_-A-G,53,l-AGU_-C,72,r-AU-C-G-_,71,l-A_-CU-G,70,l-CU_-AG,69,r-ACU-G_,67,r-A_-CU-G,117,r-AG-CU-_,116,r-AG-CU-_,115,l-ACU-G_,114,r-ACG-U_,113,r-ACU_-G,144,r-AGU-C-_,143,r-AU-C-G-_,142,l-ACG-U_,140,r-AGU_-C,139,l-ACU_-G,163,r-AGU-C-_,162,l-A-C-G-U-_,161,r-CU_-AG,157,l-CU_-AG,156,r-ACU_-G,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,196,l-ACGU-_,178,l-ACGU-_,176,l-CGU-A_,229,r-AG-C-U-_,228,l-AG-C-U-_,225,r-AG-CU-_,224,l-A_-GU-C,262,r-AC-GU-_,261,l-AG-CU-_,260,r-AG-CU-_,259,r-AG-CU-_,255,l-ACGU-_
  8. store-pair,57,r-AG-C-U-_,56,l-ACU_-G,55,r-A_-GU-C,54,r-CU_-A-G,53,l-AGU_-C,72,r-AU-C-G-_,71,l-A_-CU-G,70,l-A_-CU-G,69,r-ACU-G_,67,r-A_-CU-G,117,r-AG-CU-_,116,r-AG-CU-_,115,l-AG-CU-_,113,r-ACU_-G,112,r-ACU_-G,144,r-AGU-C-_,143,r-AU-C-G-_,142,l-ACG-U_,141,r-ACU-G_,140,r-AGU_-C,139,l-ACU_-G,163,r-AGU-C-_,162,l-AG-C-U-_,161,r-CU_-AG,157,l-CU_-AG,156,r-ACU_-G,154,l-ACU_-G,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,196,l-ACGU-_,177,l-AGU-C-_,176,l-CGU-A_,229,r-A_-GU-C,228,l-AG-C-U-_,227,r-AG-CU-_,225,r-AG-CU-_,224,l-AG_-CU,262,r-AC-GU-_,261,l-AG-CU-_,260,r-AG-CU-_,259,r-AG-CU-_,258,r-AGU-C_,255,l-ACGU-_
  9. sub,222,61/sub,53,202/sub,67,162/sub,202,102/sub,175,430
  10. store-pair,57,r-AG-C-U-_,56,l-ACU-G-_,55,r-A-C-G-U-_,54,r-CU_-A-G,53,l-AU_-C-G,72,r-AU-C-G-_,71,r-AU-C-G-_,70,l-A_-CU-G,69,r-A_-CU-G,67,r-U_-A-C-G,117,r-AG-CU-_,116,r-AG-CU-_,115,l-AG-CU-_,114,r-ACG-U_,113,r-ACU_-G,112,r-ACU_-G,108,r-ACU_-G,144,r-AGU-C-_,143,r-AU-C-G-_,142,l-ACU-G-_,141,r-ACU-G_,140,r-AGU-C-_,139,l-ACU_-G,163,r-AGU-C-_,162,l-A-C-G-U-_,161,r-CU_-AG,159,l-AGU-C_,157,l-CU-A-G-_,156,r-ACU_-G,154,l-ACU_-G,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,196,l-ACGU-_,191,r-AGU-C_,178,l-ACGU-_,177,l-AGU-C-_,176,l-CGU-A_,229,r-AG-C-U-_,228,l-AG-C-U-_,227,r-AG-CU-_,225,r-AG-CU-_,224,l-A_-GU-C,223,r-ACU-G_,262,r-AC-GU-_,261,l-AG-CU-_,260,r-AG-CU-_,259,r-AG-CU-_,258,l-AG-CU-_,256,r-ACGU-_,255,l-ACGU-_
• RF00017
  1. hmm (compacted-type)
  2. hmm (expanded-type)
  3. store-pair,13,l-CU_-AG,33,l-AG-CU-_,193,r-CU_-AG,192,l-ACU-G_,235,r-AGU-C_
  4. store-pair,13,l-ACU-G-_,12,r-AU-C-G-_,33,l-AG-CU-_,32,l-AGU-C-_,31,l-AGU-C-_,193,r-CU_-AG,192,l-ACU-G_,191,l-ACU-G_,190,r-AG-CU-_,235,l-AU_-C-G,234,r-CGU-A_,233,r-AGU-C_,229,r-AGU_-C
  5. sub,176,75
• RF00023
  1. hmm (compact-type)
  2. hmm (expanded-type)
  3. store-pair,104,r-ACGU-_,103,l-ACGU-_,160,l-ACGU-_,159,l-ACGU-_,199,r-ACGU-_,198,l-ACGU-_,239,r-ACGU-_,238,l-ACGU-_,284,l-ACGU-_,283,r-ACGU-_,302,l-ACGU-_,299,r-AU-CG-_
  4. sub,189,100/sub,227,100
  5. sub,189,100/sub,227,100/sub,270,100
• RF00029
  1. hmm (expanded-type)
  2. store-pair,24,l-A-C-G-U-_,42,l-A-C-G-U-_
  3. sub,20,30
  4. store-pair,23,l-A-C-G-U-_,24,l-A-C-G-U-_,41,l-A-C-G-U-_,42,l-A-C-G-U-_
• RF00059
  1. hmm (expanded type)
  2. store-pair,44,l-A-C-G-U-_,77,l-A-C-G-U-_,116,l-A-C-G-U-_,117,l-A-C-G-U-_
  3. sub,113,40
  4. store-pair,44,l-A-C-G-U-_,77,l-A-C-G-U-_,115,l-A-C-G-U-_,116,l-A-C-G-U-_,117,l-A-C-G-U-_
  5. sub,103,100
• RF00168
  1. hmm (expanded-type)
  2. store-pair,56,l-ACGU-_,54,l-AG_-CU,93,l-ACU-G_,92,l-CGU-A-_,110,r-AG-CU-_,109,l-ACU-G_,125,l-ACG-U-_,124,r-AC-GU-_
  3. sub,86,40
  4. sub,100,65
  5. sub,118,70/sub,100,65
• RF00174
  1. store-pair,41,r-CU_-AG,40,r-ACU-G_,79,l-ACU_-G,78,r-AGU_-C,93,l-ACU-G_,92,r-AGU_-C,91,l-ACG-U_,154,r-ACU-G-_,153,r-AGU-C_
  2. store-pair,41,l-AG-CU-_,40,r-ACU-G_,39,l-AGU-C_,79,l-ACU-G-_,78,r-AGU-C-_,76,r-ACU-G_,93,l-ACU-G_,92,r-AGU-C-_,91,l-AC-G-U-_,154,r-ACU-G-_,153,r-A-C-G-U-_,152,l-ACU-G_
  3. store-pair,41,l-AG-CU-_,40,l-AGU-C-_,39,r-CU-A-G-_,79,l-ACU-G-_,78,r-AGU-C-_,77,l-AG_-CU,76,r-ACU-G_,75,r-CU_-AG,93,r-ACU-G-_,92,r-AGU-C-_,91,r-A-C-G-U-_,154,r-CU-A-G-_,153,l-AC-GU-_,152,r-AG-CU-_,150,r-ACU_-G
  4. store-pair,41,r-CU-A-G-_,40,l-AG-C-U-_,39,r-CU-A-G-_,79,l-ACU-G-_,78,r-AGU-C-_,77,r-AU-C_-G,76,r-AU-C_-G,75,r-CU_-AG,93,r-ACU-G-_,92,r-AG-C-U-_,91,r-A-C-G-U-_,154,r-ACU-G-_,153,r-A-C-G-U-_,152,r-AG-CU-_,150,r-ACU_-G,142,l-ACU-G-_
  5. sub,133,240/sub,91,40
  6. sub,133,240/sub,75,430
  7. sub,101,450
• tRNAscan-SE archaea
  1. hmm (expanded-type)
  2. store-pair,19,r-CGU-A_,18,l-ACG-U_,37,r-A-C-G-U-_,57,l-ACGU-_,52,l-ACGU-_,70,r-AGU_-C,69,r-AGU-C-_
  3. store-pair,19,r-AU-CG-_,18,l-AG-C-U-_,37,l-GU-A-C-_,35,r-AGU-C_,34,r-ACU-G_,57,l-ACGU-_,54,r-ACGU-_,53,l-ACGU-_,52,l-ACGU-_,70,r-AGU_-C,69,r-AGU_-C,68,r-AGU-C-_
  4. store-pair,19,r-AU-CG-_,18,l-AG-C-U-_,17,l-AG-C-U-_,37,l-GU-A-C-_,36,l-ACU-G-_,35,r-AGU-C_,34,r-ACU-G_,57,l-ACGU-_,54,r-ACGU-_,53,l-ACGU-_,52,l-ACGU-_,51,l-ACGU-_,70,r-AGU-C-_,69,r-AGU-C-_,68,r-AGU-C-_,67,r-ACU-G_
  5. sub,16,87/sub,66,45/sub,51,24
  6. sub,33,250/sub,16,87/sub,66,45/sub,51,24
• tRNAscan-SE eubacterial
  1. store-pair,18,l-AG-C_-U,37,r-A_-C-G-U,57,l-ACGU-_,55,l-ACGU-_,70,l-ACU_-G,69,l-ACU_-G
  2. store-pair,19,r-ACU_-G,18,l-ACG-U_,17,r-ACU_-G,37,l-A-C-G-U-_,36,l-ACU_-G,56,l-ACGU-_,55,l-ACGU-_,54,r-ACGU-_,70,l-ACU_-G,69,l-ACU_-G,68,l-CU_-AG
  3. store-pair,19,r-ACU-G-_,18,l-AG-C_-U,17,r-ACU_-G,37,r-A_-C-G-U,36,l-ACU_-G,35,l-AC-U_-G,56,l-ACGU-_,55,l-ACGU-_,54,r-ACGU-_,53,r-ACGU-_,70,l-ACU_-G,69,l-ACU_-G,68,l-CU_-AG,67,l-AG_-CU
  4. store-pair,19,r-ACU_-G,18,l-AC-G-U-_,17,r-ACU_-G,16,l-ACU_-G,37,r-A_-C-G-U,35,l-A_-C-G-U,34,r-A_-CU-G,56,l-ACGU-_,55,l-ACGU-_,54,r-ACGU-_,53,r-ACGU-_,52,l-ACGU-_,70,l-ACU_-G,69,l-ACU_-G,68,l-A-C-G-U-_,67,l-AG_-CU
  5. sub,33,56/sub,16,56/sub,51,40
  6. sub,33,56/sub,66,63/sub,51,40/sub,16,56
• tRNAscan-SE eukaryotic nuclear (used for Drosophila, C. elegans, and human).
  1. store-pair,15,r-A-C-G-U-_,34,r-AG-C_-U,32,r-AU_-CG,51,l-ACGU-_,50,r-ACGU-_,67,l-ACU_-G,65,r-AG-U_-C
  2. store-pair,16,l-AG_-CU,15,r-A-C-G-U-_,14,r-CU_-A-G,34,r-A_-C-G-U,32,r-A_-C-G-U,31,l-AG_-CU,54,l-ACGU-_,51,l-ACGU-_,50,r-ACGU-_,49,l-ACGU-_,48,r-ACGU-_,67,l-ACU_-G,66,r-AGU_-C,65,l-ACU-G_,64,r-ACU-G_,63,r-AG_-CU
  3. sub,63,48/sub,48,32/sub,13,63
  4. sub,63,48/sub,30,500/sub,13,63
• tRNAscan-SE eukaryotic nuclear selenocysteine (this is an easy family that does not require the techniques presented in this paper)
  1. hmm (expanded type)

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.