For Genome MJ, Tables with Specific Analysis

Table Name Size (kb), Format Links Fields (keys bold) Description
tm segs 31 k, tab delim. data, head id_, start_I, stop_n, energy_f 

Transmembrane segments. 
(version 2, revised 971113)
tm histo 1 k, tab delim. data, head ntm_I, prots_n 

Histogram of frequency of transmembrane segments.
signal segs 3 k, tab delim. data, head id_, start_I, stop_n 

Signal sequences.
seq MBY pdb MBY lcl MBY tms MBY lnk STAT 1 k, tab delim. data, head stat_, value 

This are the statistics from masking the fasta file seq_MBY_pdb_MBY_lcl_MBY_tms with
the mask linkers to generate the masked fasta file seq_MBY_pdb_MBY_lcl_MBY_tms_MBY_lnk.
MASKED_CHARS  = number of characters masked with the application of this mask.
Masked_Seqs   = number of sequences masked with the application of this mask.
Masking_Segs  = number of segments used in the application of the mask
seq MBY pdb MBY lcl MBY tms MBY lnk COMP 1 k, tab delim. data, head aa_, count_n 

This is the aa composition of the 
masked file from masking the fasta file seq_MBY_pdb_MBY_lcl_MBY_tms with
the mask linkers to generate the masked fasta file seq_MBY_pdb_MBY_lcl_MBY_tms_MBY_lnk.
seq MBY pdb MBY lcl MBY tms MBY lnk 509 k, fasta data, head gid_, masked_seq 

This fasta file is the result of masking seq_MBY_pdb_MBY_lcl_MBY_tms 
with the mask linkers
minscop soluble matches no overlap 16 k, tab delim. data, head gid_, TargStart_I, TargStop_n, did, fids, QryStart_n, QryStop_n, ev_f, swsc_n, swid_f 

These are the good matches to an e-value cutoff of .01 
for just the soluble proteins, scop classes 1-5,7
This table is the result of filtering out the matches from 
minscop_soluble_matches that hit the same sequence on the genome.
id ntm 19 k, tab delim. data, head id_, signalp, ntm_n 

This table contains the number of transmembrane segments for each ORF.
Its definition of TM-segment is after filtering. 
It also has signal sequence data, based on simple criteria.
fold occurrence 4 k, tab delim. data, head fold_, count 

Number of times each fold (represented by two scop fid numbers) occurs in genome MJ
This table should be sorted into a standard order.
all masks 249 k, tab delim. data, head gid_, start_I, stop_n, tool_, score 

This file concatenates the results of 
creating all the masks for genome MJ.
aafreq histo 1 k, tab delim. data, head aa_, freq_n 

Histogram of frequency of the various amino acids
alla segs 5 k, tab delim. data, head id_, start_I, stop_n 

all-a segments
allb segs 2 k, tab delim. data, head id_, start_I, stop_n 

all-b segments
characterized domains 28 k, tab delim. data, head id_, start_I, stop_n 

Already characterized domains (the borders between
linker regions).
fid12 count 3 k, tab delim. data, head fid12_, count_n, foldname 

top-10 counts
full len segs 22 k, tab delim. data, head id_, start_I, stop_n 

Full length segments.
genome v minscop 456 k, tab delim. data, head did_, gid_, TargStart_I, TargStop_n, QryStart_n, QryStop_n, ev_f, swsc_n, swid_f 

Result of running genome MJ against Ted's minscop (scop 1.35)
genome v pdb40 132 7 k, tab delim. data, head did_, gid_, TargStart_i, TargStop_i, QryStart_i, QryStop_i, ev_r, swsc_f 

Result of running genome MJ agains pdb40d-1.32
The swsc_f column is really ident. 
Using an e-value cutoff of .001
genome v pdb40d135 560 k, tab delim. data, head did_, gid_, TargStart_I, TargStop_n, QryStart_n, QryStop_n, ev_f, swsc_n, swid_f 

Result of running genome MJ agains pdb40d-1.35
gorss 509 k, fasta data, head
gorss MBY nul 509 k, fasta data, head gid_, masked_seq 

This fasta file is the result of masking gorss 
with the mask full_len_segs
gorss MBY nul COMP 1 k, tab delim. data, head aa_, count_n 

This is the aa composition of the 
masked file from masking the fasta file gorss with
the mask full_len_segs to generate the masked fasta file gorss_MBY_nul.
gorss MBY nul STAT 1 k, tab delim. data, head stat_, value 

This are the statistics from masking the fasta file gorss with
the mask full_len_segs to generate the masked fasta file gorss_MBY_nul.
MASKED_CHARS  = number of characters masked with the application of this mask.
Masked_Seqs   = number of sequences masked with the application of this mask.
Masking_Segs  = number of segments used in the application of the mask
gorss MBY ucd 509 k, fasta data, head gid_, masked_seq 

This fasta file is the result of masking gorss 
with the mask unchar_domains
gorss MBY ucd COMP 1 k, tab delim. data, head aa_, count_n 

This is the aa composition of the 
masked file from masking the fasta file gorss with
the mask unchar_domains to generate the masked fasta file gorss_MBY_ucd.
gorss MBY ucd STAT 1 k, tab delim. data, head stat_, value 

This are the statistics from masking the fasta file gorss with
the mask unchar_domains to generate the masked fasta file gorss_MBY_ucd.
MASKED_CHARS  = number of characters masked with the application of this mask.
Masked_Seqs   = number of sequences masked with the application of this mask.
Masking_Segs  = number of segments used in the application of the mask
id ntm nofilt 19 k, tab delim. data, head id_, signalp, ntm_n 

This table contains data on whether there is a signal sequence
and the number of transmembrane segments.
(version 2, revised 971113).
(Renamed table on 980101: id_ntm --> id_ntm_nofilt)
linkers 24 k, tab delim. data, head id_, start_I, stop_n 

Linker regions between two other defined segments, 
which are less in length than 50
low complexity long 28 k, tab delim. data, head id_, start_I, stop_n, cplxity_f 

Low complexity regions generated with the
following seg command: seg/seg tmp.fa 45 3.4 3.75 -l
low complexity short 44 k, tab delim. data, head id_, start_I, stop_n, cplxity_f 

Low complexity regions generated with the
following seg command: seg/seg tmp.fa 25 3.0 3.3 -l
minscop occurrence 10 k, tab delim. data, head did_, count 

Number of times each minscop domain id (did) occurs in genome MJ
This table should be sorted into a standard order and contain 990 entries.
minscop soluble matches 17 k, tab delim. data, head gid_, TargStart_I, TargStop_n, did, fids, QryStart_n, QryStop_n, ev_f, swsc_n, swid_f 

These are the good matches to an e-value cutoff of .01 
for just the soluble proteins, scop classes 1-5,7
This is with a year cutoff of 97
minscop soluble matches overlap 2 k, tab delim. data, head gid_, TargStart_I, TargStop_n, did, fids, QryStart_n, QryStop_n, ev_f, swsc_n, swid_f 

These are the good matches to an e-value cutoff of .01 
for just the soluble proteins, scop classes 1-5,7
This table is the matches from 
minscop_soluble_matches that hit the same sequence on the genome. 
That is, it contains duplicate matches that should not be used.
null mask 1 k, tab delim. data, head
pdb40d135 soluble matches 35 k, tab delim. data, head gid_, TargStart_I, TargStop_n, did, fids, QryStart_n, QryStop_n, ev_f, swsc_n, swid_f 

These are the good matches to an e-value cutoff of .01 
for just the soluble proteins, scop classes 1-5,7
seq 541 k, Hidden data, head - 

-
seq MBY cdo 509 k, fasta data, head gid_, masked_seq 

This fasta file is the result of masking seq 
with the mask characterized_domains
seq MBY cdo COMP 1 k, tab delim. data, head aa_, count_n 

This is the aa composition of the 
masked file from masking the fasta file seq with
the mask characterized_domains to generate the masked fasta file seq_MBY_cdo.
seq MBY cdo STAT 1 k, tab delim. data, head stat_, value 

This are the statistics from masking the fasta file seq with
the mask characterized_domains to generate the masked fasta file seq_MBY_cdo.
MASKED_CHARS  = number of characters masked with the application of this mask.
Masked_Seqs   = number of sequences masked with the application of this mask.
Masking_Segs  = number of segments used in the application of the mask
seq MBY lcl 509 k, fasta data, head gid_, masked_seq 

This fasta file is the result of masking seq 
with the mask low_complexity_long
seq MBY lcl COMP 1 k, tab delim. data, head aa_, count_n 

This is the aa composition of the 
masked file from masking the fasta file seq with
the mask low_complexity_long to generate the masked fasta file seq_MBY_lcl.
seq MBY lcl STAT 1 k, tab delim. data, head stat_, value 

This are the statistics from masking the fasta file seq with
the mask low_complexity_long to generate the masked fasta file seq_MBY_lcl.
MASKED_CHARS  = number of characters masked with the application of this mask.
Masked_Seqs   = number of sequences masked with the application of this mask.
Masking_Segs  = number of segments used in the application of the mask
seq MBY lcs 4 k, Bad! data, head gid_, masked_seq 

This fasta file is the result of masking seq 
with the mask low_complexity_short
seq MBY lcs COMP 1 k, tab delim. data, head aa_, count_n 

This is the aa composition of the 
masked file from masking the fasta file seq with
the mask low_complexity_short to generate the masked fasta file seq_MBY_lcs.
seq MBY lcs STAT 1 k, tab delim. data, head stat_, value 

This are the statistics from masking the fasta file seq with
the mask low_complexity_short to generate the masked fasta file seq_MBY_lcs.
seq MBY lnk 509 k, fasta data, head gid_, masked_seq 

This fasta file is the result of masking seq 
with the mask linkers
seq MBY lnk COMP 1 k, tab delim. data, head aa_, count_n 

This is the aa composition of the 
masked file from masking the fasta file seq with
the mask linkers to generate the masked fasta file seq_MBY_lnk.
seq MBY lnk STAT 1 k, tab delim. data, head stat_, value 

This are the statistics from masking the fasta file seq with
the mask linkers to generate the masked fasta file seq_MBY_lnk.
MASKED_CHARS  = number of characters masked with the application of this mask.
Masked_Seqs   = number of sequences masked with the application of this mask.
Masking_Segs  = number of segments used in the application of the mask
seq MBY nul 509 k, fasta data, head gid_, masked_seq 

This fasta file is the result of masking seq 
with the mask full_len_segs
seq MBY nul COMP 1 k, tab delim. data, head aa_, count_n 

This is the aa composition of the 
masked file from masking the fasta file seq with
the mask full_len_segs to generate the masked fasta file seq_MBY_nul.
seq MBY nul STAT 1 k, tab delim. data, head stat_, value 

This are the statistics from masking the fasta file seq with
the mask full_len_segs to generate the masked fasta file seq_MBY_nul.
MASKED_CHARS  = number of characters masked with the application of this mask.
Masked_Seqs   = number of sequences masked with the application of this mask.
Masking_Segs  = number of segments used in the application of the mask
seq MBY pdb 509 k, fasta data, head gid_, masked_seq 

This fasta file is the result of masking seq 
with the mask minscop_soluble_matches
seq MBY pdb COMP 1 k, tab delim. data, head aa_, count_n 

This is the aa composition of the 
masked file from masking the fasta file seq with
the mask minscop_soluble_matches to generate the masked fasta file seq_MBY_pdb.
seq MBY pdb MBY lcl 509 k, fasta data, head gid_, masked_seq 

This fasta file is the result of masking seq_MBY_pdb 
with the mask low_complexity_long
seq MBY pdb MBY lcl COMP 1 k, tab delim. data, head aa_, count_n 

This is the aa composition of the 
masked file from masking the fasta file seq_MBY_pdb with
the mask low_complexity_long to generate the masked fasta file seq_MBY_pdb_MBY_lcl.
seq MBY pdb MBY lcl MBY lcs 6 k, Bad! data, head gid_, masked_seq 

This fasta file is the result of masking seq_MBY_pdb_MBY_lcl 
with the mask low_complexity_long
seq MBY pdb MBY lcl MBY lcs COMP 1 k, tab delim. data, head aa_, count_n 

This is the aa composition of the 
masked file from masking the fasta file seq_MBY_pdb_MBY_lcl with
the mask low_complexity_long to generate the masked fasta file seq_MBY_pdb_MBY_lcl_MBY_lcs.
seq MBY pdb MBY lcl MBY lcs MBY tms 4 k, Bad! data, head gid_, masked_seq 

This fasta file is the result of masking seq_MBY_pdb_MBY_lcl_MBY_lcs 
with the mask tm_segs
seq MBY pdb MBY lcl MBY lcs MBY tms COMP 1 k, tab delim. data, head aa_, count_n 

This is the aa composition of the 
masked file from masking the fasta file seq_MBY_pdb_MBY_lcl_MBY_lcs with
the mask tm_segs to generate the masked fasta file seq_MBY_pdb_MBY_lcl_MBY_lcs_MBY_tms.
seq MBY pdb MBY lcl MBY lcs MBY tms STAT 1 k, tab delim. data, head stat_, value 

This are the statistics from masking the fasta file seq_MBY_pdb_MBY_lcl_MBY_lcs with
the mask tm_segs to generate the masked fasta file seq_MBY_pdb_MBY_lcl_MBY_lcs_MBY_tms.
seq MBY pdb MBY lcl MBY lcs STAT 1 k, tab delim. data, head stat_, value 

This are the statistics from masking the fasta file seq_MBY_pdb_MBY_lcl with
the mask low_complexity_long to generate the masked fasta file seq_MBY_pdb_MBY_lcl_MBY_lcs.
seq MBY pdb MBY lcl MBY tms 509 k, fasta data, head gid_, masked_seq 

This fasta file is the result of masking seq_MBY_pdb_MBY_lcl 
with the mask tm_segs
seq MBY pdb MBY lcl MBY tms COMP 1 k, tab delim. data, head aa_, count_n 

This is the aa composition of the 
masked file from masking the fasta file seq_MBY_pdb_MBY_lcl with
the mask tm_segs to generate the masked fasta file seq_MBY_pdb_MBY_lcl_MBY_tms.
seq MBY pdb MBY lcl MBY tms MBY lnk MBY alp 509 k, fasta data, head gid_, masked_seq 

This fasta file is the result of masking seq_MBY_pdb_MBY_lcl_MBY_tms_MBY_lnk 
with the mask alla_segs
seq MBY pdb MBY lcl MBY tms MBY lnk MBY alp COMP 1 k, tab delim. data, head aa_, count_n 

This is the aa composition of the 
masked file from masking the fasta file seq_MBY_pdb_MBY_lcl_MBY_tms_MBY_lnk with
the mask alla_segs to generate the masked fasta file seq_MBY_pdb_MBY_lcl_MBY_tms_MBY_lnk_MBY_alp.
seq MBY pdb MBY lcl MBY tms MBY lnk MBY alp MBY bet 509 k, fasta data, head gid_, masked_seq 

This fasta file is the result of masking seq_MBY_pdb_MBY_lcl_MBY_tms_MBY_lnk_MBY_alp 
with the mask allb_segs
seq MBY pdb MBY lcl MBY tms MBY lnk MBY alp MBY bet COMP 1 k, tab delim. data, head aa_, count_n 

This is the aa composition of the 
masked file from masking the fasta file seq_MBY_pdb_MBY_lcl_MBY_tms_MBY_lnk_MBY_alp with
the mask allb_segs to generate the masked fasta file seq_MBY_pdb_MBY_lcl_MBY_tms_MBY_lnk_MBY_alp_MBY_bet.
seq MBY pdb MBY lcl MBY tms MBY lnk MBY alp MBY bet STAT 1 k, tab delim. data, head stat_, value 

This are the statistics from masking the fasta file seq_MBY_pdb_MBY_lcl_MBY_tms_MBY_lnk_MBY_alp with
the mask allb_segs to generate the masked fasta file seq_MBY_pdb_MBY_lcl_MBY_tms_MBY_lnk_MBY_alp_MBY_bet.
MASKED_CHARS  = number of characters masked with the application of this mask.
Masked_Seqs   = number of sequences masked with the application of this mask.
Masking_Segs  = number of segments used in the application of the mask
seq MBY pdb MBY lcl MBY tms MBY lnk MBY alp STAT 1 k, tab delim. data, head stat_, value 

This are the statistics from masking the fasta file seq_MBY_pdb_MBY_lcl_MBY_tms_MBY_lnk with
the mask alla_segs to generate the masked fasta file seq_MBY_pdb_MBY_lcl_MBY_tms_MBY_lnk_MBY_alp.
MASKED_CHARS  = number of characters masked with the application of this mask.
Masked_Seqs   = number of sequences masked with the application of this mask.
Masking_Segs  = number of segments used in the application of the mask
seq MBY pdb MBY lcl MBY tms STAT 1 k, tab delim. data, head stat_, value 

This are the statistics from masking the fasta file seq_MBY_pdb_MBY_lcl with
the mask tm_segs to generate the masked fasta file seq_MBY_pdb_MBY_lcl_MBY_tms.
MASKED_CHARS  = number of characters masked with the application of this mask.
Masked_Seqs   = number of sequences masked with the application of this mask.
Masking_Segs  = number of segments used in the application of the mask
seq MBY pdb MBY lcl STAT 1 k, tab delim. data, head stat_, value 

This are the statistics from masking the fasta file seq_MBY_pdb with
the mask low_complexity_long to generate the masked fasta file seq_MBY_pdb_MBY_lcl.
MASKED_CHARS  = number of characters masked with the application of this mask.
Masked_Seqs   = number of sequences masked with the application of this mask.
Masking_Segs  = number of segments used in the application of the mask
seq MBY pdb MBY tms 1 k, Bad! data, head gid_, masked_seq 

This fasta file is the result of masking seq_MBY_pdb 
with the mask tm_segs
seq MBY pdb MBY tms COMP 1 k, tab delim. data, head aa_, count_n 

This is the aa composition of the 
masked file from masking the fasta file seq_MBY_pdb with
the mask tm_segs to generate the masked fasta file seq_MBY_pdb_MBY_tms.
seq MBY pdb MBY tms STAT 1 k, tab delim. data, head stat_, value 

This are the statistics from masking the fasta file seq_MBY_pdb with
the mask tm_segs to generate the masked fasta file seq_MBY_pdb_MBY_tms.
seq MBY pdb STAT 1 k, tab delim. data, head stat_, value 

This are the statistics from masking the fasta file seq with
the mask minscop_soluble_matches to generate the masked fasta file seq_MBY_pdb.
MASKED_CHARS  = number of characters masked with the application of this mask.
Masked_Seqs   = number of sequences masked with the application of this mask.
Masking_Segs  = number of segments used in the application of the mask
seq MBY tms 509 k, fasta data, head gid_, masked_seq 

This fasta file is the result of masking seq 
with the mask tm_segs
seq MBY tms COMP 1 k, tab delim. data, head aa_, count_n 

This is the aa composition of the 
masked file from masking the fasta file seq with
the mask tm_segs to generate the masked fasta file seq_MBY_tms.
seq MBY tms STAT 1 k, tab delim. data, head stat_, value 

This are the statistics from masking the fasta file seq with
the mask tm_segs to generate the masked fasta file seq_MBY_tms.
MASKED_CHARS  = number of characters masked with the application of this mask.
Masked_Seqs   = number of sequences masked with the application of this mask.
Masking_Segs  = number of segments used in the application of the mask
seq MBY ucd 509 k, fasta data, head gid_, masked_seq 

This fasta file is the result of masking seq 
with the mask unchar_domains
seq MBY ucd COMP 1 k, tab delim. data, head aa_, count_n 

This is the aa composition of the 
masked file from masking the fasta file seq with
the mask unchar_domains to generate the masked fasta file seq_MBY_ucd.
seq MBY ucd STAT 1 k, tab delim. data, head stat_, value 

This are the statistics from masking the fasta file seq with
the mask unchar_domains to generate the masked fasta file seq_MBY_ucd.
MASKED_CHARS  = number of characters masked with the application of this mask.
Masked_Seqs   = number of sequences masked with the application of this mask.
Masking_Segs  = number of segments used in the application of the mask
seq lengths 19 k, tab delim. data, head gid_, length_n 

Length of each sequence in genome.
sfam occurrence 8 k, tab delim. data, head sfam_, count 

Number of times each sfam (represented by three scop fid numbers) occurs in genome MJ
This table should be sorted into a standard order.
tm segs filtered 11 k, tab delim. data, head id_, start_I, stop_n, energy_f 

Transmembrane segment definitions after removing pdb matches and (most
importantly) low-complexity regions. The tm_segs table is just
the raw data.
This is based on looking at the masked the file seq_MBY_pdb_MBY_lcl_MBY_tms_MBY_lnk for the TM
segments (annotated with a 3).
tmp genome v pdb40 132 4 k, tab delim. data, head did_, gid_, fid1, fid2 

temp table
unchar domains 21 k, tab delim. data, head id_, start_I, stop_n 

Linker regions between two other defined segments, 
which are greater in length than 50 
That is, these are uncharacterized protein domains.

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