(Local) PROFILESEGMENTS of: HS7B_DROME check: 1429 from: 1 to: 68
ID HS7B_DROME STANDARD; PRT; 68 AA.
AC P11146;
DT 01-JUL-1989 (REL. 11, CREATED)
DT 01-JUL-1989 (REL. 11, LAST SEQUENCE UPDATE)
DT 01-APR-1993 (REL. 25, LAST ANNOTATION UPDATE)
DE HEAT SHOCK 70 KD PROTEIN COGNATE 2 (HEAT SHOCK 70 KD PROTEIN 87D) . . .
to: hsp70.prf check: 8876 from: 1 to: 718
(Peptide) PROFILEMAKE v4.50 of: hsp70.msf{*} Length: 718
Sequences: 28 MaxScore: 2172.36 October 11, 1996 11:41
Gap: 1.00 Len: 1.00
GapRatio: 0.33 LenRatio: 0.10
hsp70.msf{Hs70_Plafa} From: 1 To: 718 Weight: 1.00
hsp70.msf{Hs70_Thean} From: 1 To: 718 Weight: 1.00 . . .
Profile: hsp70.prf
Gap Weight: 24.000 Average Match: 1.132
Length Weight: 0.270 Average Mismatch: -1.028
Quality: 240.64 Length: 65
Ratio: 3.76 Gaps: 1
hs7b_drome x hsp70.prf October 14, 1996 14:53 ..
. . . . .
S 5 PAIGIDLGTTYSCVGVWQNSKVEIIANDQGNRTTPSYVAFN.ETERLIGD 53
|:||||||||||||:::. .||||||||||||||||||| ::||||||
P 31 PAIGIBLGTTYSCVGVFQHGKVEIIANBQGNRTTPSYVAFTQBTERLIGB 80
.
//////////////////////////////////////////////////////////////
(Local) PROFILESEGMENTS of: HS7C_HUMAN check: 4205 from: 1 to: 646
ID HS7C_HUMAN STANDARD; PRT; 646 AA.
AC P11142;
DT 01-JUL-1989 (REL. 11, CREATED)
DT 01-JUL-1989 (REL. 11, LAST SEQUENCE UPDATE)
DT 01-FEB-1996 (REL. 33, LAST ANNOTATION UPDATE)
DE HEAT SHOCK COGNATE 71 KD PROTEIN. . . .
to: hsp70.prf check: 8876 from: 1 to: 718
(Peptide) PROFILEMAKE v4.50 of: hsp70.msf{*} Length: 718
Sequences: 28 MaxScore: 2172.36 October 11, 1996 11:41
Gap: 1.00 Len: 1.00
GapRatio: 0.33 LenRatio: 0.10
hsp70.msf{Hs70_Plafa} From: 1 To: 718 Weight: 1.00
hsp70.msf{Hs70_Thean} From: 1 To: 718 Weight: 1.00 . . .
Profile: hsp70.prf
Gap Weight: 24.000 Average Match: 1.132
Length Weight: 0.270 Average Mismatch: -1.028
Quality: 2056.47 Length: 665
Ratio: 3.18 Gaps: 12
hs7c_human x hsp70.prf October 14, 1996 14:53 ..
. . . . .
S 1 MSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFT.DTER 49
. |:||||||||||||::::..|||||||||||||||||||| |:||
P 27 MTKGPAIGIBLGTTYSCVGVFQHGKVEIIANBQGNRTTPSYVAFTQBTER 76
. . . . .
//////////////////////////////////////////////////////////////
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INPUT FILES
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ProfileSegments reads the ProfileSearch output file in order to obtain the names of the sequences, the name of the profile, and the gap creation and gap extension penalties. You can tell ProfileSegments to ignore any of the sequence files in the list by editing this file. To do this, insert an exclamation point (!) as the first character of the line that you wish to comment out. If the profile that was used in ProfileSearch cannot be identified and read correctly from the information in the text heading of the input file, ProfileSegments complains and stops.
If the gap creation penalty and gap extension penalty cannot be read correctly from the information in the text heading of the input file, ProfileSegments calculates values from the profile itself, using the maximum match value that is present in the profile: 3 x MaxMatch for the gap creation penalty and MaxMatch / 30 for the gap extension penalty.
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RELATED PROGRAMS
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PileUp creates a multiple sequence alignment from a group of related sequences. LineUp is a multiple sequence editor used to create multiple sequence alignments. Pretty displays multiple sequence alignments.
ProfileMake makes a profile from a multiple sequence alignment. ProfileSearch uses the profile to search a database for sequences with similarity to the group of aligned sequences. ProfileSegments displays optimal alignments between each sequence in the ProfileSearch output list and the group of aligned sequences (represented by the profile consensus). ProfileGap makes optimal alignments between one or more sequences and a group of aligned sequences represented as a profile. ProfileScan finds structural and sequence motifs in protein sequences, using predetermined parameters to determine significance.
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RESTRICTIONS
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We have little experience using nucleotide sequences with profile analysis.
The surface of comparison (see the entry for BestFit in the Program Manual) may not be more than some value set within the program (5.5 million at most institutions). Profiles may not be longer than 1,000 residues or bases. Sequences that are too long for the surface of comparison are divided into smaller segments that are aligned separately (see the CONSIDERATIONS topic, below).
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ALGORITHM
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See the Profile Analysis Essay for an introduction to associating distantly related proteins and finding structural motifs.
ProfileSegments reads the profile, the profile's consensus sequence, and the set of sequences in the list created by ProfileSearch and then uses the same algorithm as BestFit to align each sequence to the profile. The alignment is made with the values in the profile. The display is made with the consensus sequence and values from the profile. For a detailed description of Smith and Waterman-style alignments, see the BestFit program's entry.
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CONSIDERATIONS
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There is strong reason to believe that the BestFit algorithm used by ProfileSegments is the best known way to find segments of similarity, but the best parameters must be determined empirically. Like any alignment program, ProfileSegments produces alignments that are very different depending on the scoring matrix values and gap coefficients used to make up the profile, and the gap penalties used as input to ProfileSearch.
Unless the -LIMit command line parameter is used, sequences that are too long for the surface of comparison are always divided into smaller, overlapping segments that are aligned separately. The -LIMit parameter may permit long sequences to be aligned without division. For a detailed description of the -LIMit, see the entry for BestFit in the Program Manual. Sequences longer than 32,000 are always divided and aligned as separate segments. Although ProfileGap and ProfileSegments overlap the points of division by the whole length of the profile, divided sequences may not align properly if the segment of similarity crosses the point where the sequence was divided.
The command-line parameter -GLObal makes ProfileGap and ProfileSegments display the alignment of the whole sequence to the whole profile, instead of just the most-similar segment between the sequence and the profile. This is analogous to executing a Gap between the profile and sequence.
ProfileSearch/ProfileSegments finds only the best fit of the profile to any sequence. Be aware that other regions with a lower degree of similarity to the profile may also exist in the same sequence, especially in nucleic acid sequences.
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COMMAND-LINE SUMMARY
-
All parameters for this program may be put on the command line. Use the parameter -CHEck to see the summary below and to have a chance to add things to the command line before the program executes. In the summary below, the capitalized letters in the parameter names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.
Minimal Syntax: % profilesegments [-INfile=]hsp70.pfs -Default
Prompted Parameters:
-SEQLimit=15 limit the number of alignments
[-OUTfile=]hsp70.pairs output file for the alignments
Local Data Files: None
Optional Parameters:
-LOCal aligns the best segment of similarity between
the sequence and profile (local alignment is
the default)
-GLObal aligns the whole sequence and profile (global
alignment)
-NOAVErage does not adjust alignment scores for sequence
composition
-ENDWeight penalizes end gaps like other gaps
-LIMit1=20 lets you set a gap shift limit for the sequence
-LIMit2=20 lets you set a gap shift limit for the profile
-OUTfile2=hs7t_rat.gap new file for sequence 1 with gaps added
-OUTfile3=hsp70.gap new file for the profile consensus with gaps added
-MSF[=hsp70.msf] new MSF file containing alignment of all the
sequences with the profile consensus
-PAIr=1.0,0.5,0.1 thresholds for displaying '|', ':', and '.'
-NOMONitor suppresses the screen summary for each alignment
-
-
LOCAL DATA FILES
-
None.
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OPTIONAL PARAMETERS
-
The parameters listed below can be set from the command line. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.
-
-
-GLObal
-
causes this program to make alignments using the method of Needleman and Wunsch instead of the default method of Smith and Waterman. The difference between these two methods is the same as the difference between the programs Gap and BestFit. The Needleman and Wunsch method displays the whole length of both sequences after alignment, while the Smith and Waterman method shows only the best segment of similarity from each sequence.
-
-LOCal
-
forces this program to make alignments using the default method of Smith and Waterman instead of the method of Needleman and Wunsch. The difference between these two methods is the same as the difference between the programs BestFit and Gap. The Smith and Waterman method shows only the best segment of similarity from each sequence, while the Needleman and Wunsch method displays the whole length of both sequences after alignment.
-
-NOAVErage
-
turns off the adjustment of scores for sequence composition. In the default ( -AVErage), a score due to the similarity in composition between the profile and sequence of interest is subtracted from the original alignment score.
-
-ENDWeight
-
causes the end gaps to be penalized in the same way as all other gaps. This parameter is ignored unless -GLObal is also present on the command line.
-
-LIMit1=20 and -LIMit2=20
-
lets you set gap shift limits for each sequence ( -LIMit1 sets a gap shift limit for the sequence and -LIMit2 sets a gap shift limit for the profile). When you already know of a long similarity between two sequences you can "zip" them together using this mode. The beginning coordinates for each sequence must be near the beginning of the alignment you want to see. The alignment continues so that gaps inserted do not require the sequences to get out of step by more than the gap shift limits. You can align very long sequences rapidly. The surface of comparison is still limited to one million. The size of a comparison can be predicted by multiplying the average length of the two sequences times the sum of the two shift limits.
If you add just -LIMit to the command line without supplying a value, the program prompts you to enter gap shift limits for each sequence.
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-MSF=profilename.msf
-
-
-OUTfile2=seqname.gap
-
-
-OUTfile3=profilename.gap
-
This program can write up to four different output files. The primary output file (-OUTfile1) displays a pairwise alignment between the profile consensus sequence and each of the input sequences. This file is always created unless you specify -NOOUTfile1 on the command line. If you wish to create a file in MSF format that contains a multiple alignment of the consensus profile with all of the sequences, specify -MSF on the command line. If the input file is a single sequence, you can output two new sequence files that may contain gaps to reflect the sequence-profile alignment. The gapped file for the sequence is specified by -OUTfile2 and the one for the profile consensus is specified by -OUTfile3.
Aligned sequences (in sequence files) can be displayed with GapShow.
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-PAIr=1.0,0.5,0.1
-
The paired output file from this program displays sequence similarity by putting a pipe character (|), colon (:), and period (.) between similar sequence symbols. The thresholds for the characters are determined by the values in the profile. The pipe character is put between symbols whose comparison value in the profile is at least the average positive value in the profile plus one tenth the difference between the maximum and average values in the profile. The colon character threshold is the average positive value in the profile. The period character threshold is the larger of the average positive value in the profile minus one tenth the difference between the maximum and average values, and one half the average value.
-
-NOMONitor
-
suppresses the screen summary for each alignment which reports some statistics for the alignment.
-
[ Program Manual | User's Guide | Data Files | Databases ]
Documentation Comments: doc-comments@gcg.com
Technical Support: help@gcg.com
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