Program Options for seedtop
Tao Tao, Ph.D. User Service NCBI, NLM, NIH
Table of Content

- 1. Introduction
- 2. Setup
- 3. Program options
- 4. Practical Usage
  - 4.1 Pattern specification
  - 4.2 patmatchp
  - 4.3 patternp
  - 4.4 patseedp
  - 4.5 seedp
  - 4.6 For nucleotide searches
- 5. Technical Support

1. Introduction

seedtop is a little-known program found in the NCBI standalone blast package, whose main function is to search for patterns in an input sequence or database. It has four modes of usage, which are referred to as "subprograms": two for pattern searches from a input query or database only and two for pattern initiated sequence alignment. The following table lists these subprograms, their functions, and required inputs.

Table 1.1 Subprogram Fucntion of seedtop
Program Call ¹ | Functions | Required Inputs
-p patmatch | Search for patterns in an input sequence | Pattern (-k) and sequence (-i)
-p pattern | Search for patterns in an input database | Same as above
-p patseed | Search for patterns in the query and align the query against a database | Pattern (-k), input sequence (-i), and target database (-d)
-p seed | Search for specific pattern in the query and align the query against a database | Same as above ²
NOTE: ¹ The program strings listed are for nucleotide searches. For protein searches, add lowercase p to the program name. ² The pattern file needs to have an extra HI initialed line to specify the position in the input sequence at which the pattern occurrence of interest starts.

2. Setup

Installation of the standalone blast archive is fairly easy. Once the archive is placed in a desired directory and extracted, the whole package will be installed in a newly created subdirectory called blast-2.2.13 (assuming 2.2.13 release here). All the programs, including seedtop, will be in the blast-2.2.13/bin/ subdirectory (blast-2.2.13\bin\ for PC).

Appropriate setup requires the creation of .ncbirc configuration file, which blast programs (including seedtop) read upon startup to locate the appropriate files needed. In this .ncbirc, we can specify the location of the DATA directory and the BLASTDB directory using the following lines:

> [NCBI]
> DATA=/path/data
> [BLAST]
> BLASTDB=/path/db

The [NCBI] section is used by most of the NCBI programs to locate the data directory and retrieve specific files needed (MATRIX file for example). The [BLAST] section specifies the path to the directory where databases are stored.

The db directory does not come with the NCBI setup, so one needs to create it after installation. If we place the directory anywhere, we need to change the path correspondingly. For simplicity, we suggest that it be created under the blast-2.2.13 (version # will vary for future releases) at the same level as data directory.

3. Program Options

Once the standalone BLAST package is setup, we can "cd" to the directory and issue the "seedtp -" command to display the program options for this program. Here we list each option in a table and describe its functions, argument value, and example usage.

Table 3.1
Option | -d
Function | Specifies the target database to search
Default | nr
Input format | Takes database formatted by formatdb, use name without extension
Example | To search against est_human, use: -d est_human
Note | This is not a mandatory option, search for patterns in a single input sequence does not require this option.

Table 3.2
Option | -i
Function | Specifies the input query file
Default | stdin
Input format | [File In], file name with extension
Example | To take my_pept.txt as input query, use: -i my_pept.txt
Note | To using stdin as input, either redirect or pipe the input: seedtop -k pat -p patmatchp <input_file more input_file| seedtop -k pat -p patmatchp

Table 3.3
Option | -k
Function | Specifies the input pattern (Hit File)
Default | hit_file
Input format | Complete file name with extension
Example | If the pattern file is named my_pat.txt, use: -k my_pat.txt
Note | See section 4.1 below for details.

Table 3.4
Option | -o
Function | Specifies the output file name
Default | stdout
Input format | file name with or without extension
Example | To save result in my_output, use: -o my_output
Note | Redirection or piping can be used instead.

Table 3.5
Option | -G
Function | Specifies the cost to open a gap
Default | 11
Input format | [Integer]
Example | To change this to 12, use: -G 12
Note | The choice of -M option determines the available input value for this option as well as that for -E option. Only a selected set is supported. Detailed list is in the blastall document.

Table 3.6
Option | -E
Function | Specifies the cost to extend a gap
Default | 1
Input format | [Integer]
Example | To change this to 2, use: -E 2
Note | See Table 3.5 for more information

Table 3.6
Option | -D
Function | Specifies the cost to decline alignment
Default | 99999
Input format | [Integer]
Example | N/A
Note | Functions similar to the -L option in blastpgp. If enabled, it would implement Dr. Altschul's 3-parameter gap model for scoring.

Table 3.7
Option | -X
Function | Specifies X dropoff value for gapped alignment (in bits)
Default | 15
Input format | [Integer]
Example | To increase this dropoff value to 20, use: -X 20
Note | Increasing this value may enable one to see a longer alignment

Table 3.8
Option | -S
Function | Specifies cutoff cost
Default | 30
Input format | [Integer]
Example | N/A
Note | Currently it is overridden in pseed3.c. It could allow the user to control the score threshold applied to the part of the alignment that does not include the pattern in deciding which alignment(s) to report.

Table 3.9
Option | -C
Function | Score only or not
Default | 1
Input format | [Integer]
Example | N/A
Note | This is relevant only to searches with -p seed(p) or -p patseed(p). NOT implemented yet.

Table 3.10
Option | -I
Function | Whether to Show GI's in deflines
Default | F
Input format | [T/F]
Example | To display GI in the deflines, use: -I T
Note | Relevant only to searches with -p seed(p) or -p patseed(p)

Table 3.11
Option | -e
Function | Specifies the expectation value (E) cutoff
Default | 10.0
Input format | [Real]
Example | To set this to 0.001, use: -e 0.001 or -e 1e-3
Note | Relevant only to searches with -p seed(p) or -p patseed(p)

Table 3.12
Option | -J
Function | Whether to believe the query defline or not
Default | F
Input format | [T/F]
Example | To set this to true, use: -J T
Note | To save SeqAlign object requires -J T

Table 3.13
Option | -O
Function | Specifies the output file for SeqAlign object
Default | Optional
Input format | [File Out]
Example | N/A
Note | Relevant only to searches with -p seed(p) or -p patseed(p). NOT implement yet.

Table 3.14
Option | -M
Function | Specifies which matrix file to use
Default | BLOSUM62
Input format | [String]
Example | To set matrix to PAM30, use: -M PAM30
Note | Relevant to seedp/patseedp searches, only a limited set is supported

Table 3.15
Option | -p
Function | Specifies which subprogram to run
Default | patmatchp
Input format | [String]
Example | To find protein patterns in a database, use: -p patternp
Note | Choices for nucleotide searches: patmatch, pattern, seed, and patseed Choices for protein searches: patmatchp, patternp, seedp, and patseedp

Table 3.16
Option | -r
Function | Specifies the reward for a match
Default | 10
Input format | [Integer]
Example | To increase the reward to 20, use: -r 20
Note | Relevant only to searches with -p seed(p) or -p patseed For nucleotide searches only.

Table 3.17
Option | -q
Function | Specifies the cost for a mismatch
Default | -10
Input format | [Integer]
Example | To increase the penalty to -15, use: -q -15
Note | For nucleotide search with seed/patseed only.

Table 3.18
Option | -F
Function | Whether to filter query sequence with SEG
Default | F
Input format | [T/F]
Example | To activate filter, use: -F T
Note | Relevant to seedp/patseedp searches only.

4. Execution and Practical Usage
The most useful functionalities of seedtop are patmatchp and patternp. Since patseedp does not generate the actual alignment and its function is already incorporated in blastpgp, we will not cover it here. The functionality for searching with nucleotide entries are similar to protein searches, we will only provide a couple simple examples.
4.1 Pattern specification

The pattern input file is unique for seedtop. Each pattern is specified by two lines, ID initialed for identification and PA initialed for pattern. The pattern specification uses the ProSite syntax. Multiple patterns can be used, each separated by a single line with a "/".

Single pattern specification:

> ID Cyclic nucleotide-binding domain signature 2.
> PA [LIVMF]-G-E-x-[GAS]-[LIVM]-x(5,11)-R-[STAQ]-A-x-[LIVMA]-x-[STACV].

Multiple pattern specification:

> ID Cyclic nucleotide-binding domain signature 2.
> PA [LIVMF]-G-E-x-[GAS]-[LIVM]-x(5,11)-R-[STAQ]-A-x-[LIVMA]-x-[STACV].
> /
> ID Cyclic nucleotide-binding domain signature 1
> PA [LIVM]-[VIC]-x-{H}-G-[DENQTA]-x-[GAC]-{L}-x-[LIVMFY](4)-x(2)-G

Pattern lines should be less than 100 letters long. Longer patterns can be broken up into two or more PA lines. Multiple individual patterns should be separated by a line containing a single backslash (/). Other general pattern rules can be summarized as the following:

> Symbol | Meaning
> [] | marks a single position, match to anyone in the bracket is acceptable
> (x,y) | marks a range for the residue(s) before it, matching within the range is acceptable
> (x,) | represents range with no upper limit for the residue(s) before it
> (x) | represents exact number of matches for the residue(s) before it
> {} | marks a single residue, residues in the braces should be excluded
> - | separates the individual positions in the pattern
> . | used at the end marks the end of a pattern
> > | symbol at the end marks an incomplete pattern (optional)

4.2 patmatchp

This function matches patterns found in an input pattern file and identifies the pattern occurrences in an input protein sequence. The sample command line below (given along with its output) takes an input pattern named pattern.txt, searches against the input query.aa target sequence, and saves the output in a file named query.out.

> seedtop -k pattern.txt -i query.aa -p patmatchp -o query.out
> Name Cyclic nucleotide-binding domain signature 2.
> Pattern [LIVMF]-G-E-x-[GAS]-[LIVM]-x(5,11)-R-[STAQ]-A-x-[LIVMA]-x-[STACV].
> At position 521 of query sequence
> Name Cyclic nucleotide-binding domain signature 1
> Pattern [LIVM]-[VIC]-x-{H}-G-[DENQTA]-x-[GAC]-{L}-x-[LIVMFY](4)-x(2)-G
> At position 483 of query sequence

The result only lists the pattern starting positions in the query sequence.

4.3 patternp

This function matches patterns in an input pattern file against an input database and reports back the database entries containing one or more of the input patterns as well as the pattern locations. The sample command line below (given with its partial output) takes an input pattern named pattern.txt, searches against the input refseq_protein database, the identified entries with pattern matches are saved in the output file db.out.

> seedtop -k pattern.txt -d refseq_protein -p patternp -o db.out
> seqno=892602 gi|33859524|ref|NP_034048.1|
> ID Cyclic nucleotide-binding domain signature 1
> PA [LIVM]-[VIC]-x-{H}-G-[DENQTA]-x-[GAC]-{L}-x-[LIVMFY](4)-x(2)-G
> HI (449 450) (452 454) (456 457) (459 462) (465 465)
> seqno=892873 gi|51470807|ref|XP_290552.4|
> ID Cyclic nucleotide-binding domain signature 1
> PA [LIVM]-[VIC]-x-{H}-G-[DENQTA]-x-[GAC]-{L}-x-[LIVMFY](4)-x(2)-G
> HI (374 375) (377 379) (381 382) (384 387) (390 390)

Each hit is described in the following lines:

- seqno: seqid for the database sequence with pattern matches
- ID: Pattern ID, reiterated pattern input
- PA: Pattern, reiterated pattern input
- HI: Hit position on the db sequence, regions broken up by X

4.4 patseedp

This function takes three inputs, an input pattern, a query protein sequence with the pattern, and a protein sequence database. It identifies the pattern in the query and aligns the query against the database entries that contains the same pattern. It reports the pattern position in the query, the total number of pattern occurrences in the database, and the actual database entries with pattern and alignment to the input query. Specifically, it reports the seqid of the database entry, its alignment (with the query) E-value, scores, and pattern position.

> seedtop -k pattern.txt -d refseq_protein -p patseedp -o pat_db.out -i query_aa.txt
> 1 occurrence(s) of pattern in query
> Name Cyclic nucleotide-binding domain signature 2.
> Pattern [LIVMF]-G-E-x-[GAS]-[LIVM]-x(5,11)-R-[STAQ]-A-x-[LIVMA]-x-[STACV].
> At position 488 of query sequence
> effective database length=3.1e+008
> pattern probability=3.4e-008
> lengthXprobability=1.0e+001
> Number of occurrences of pattern in the database is 265
> 892602 gi|33859524|ref|NP_034048.1|
> 0 Total Score 3279 Outside Pattern Score 3162 Match start in db seq 488
> Extent in query seq 1 631 Extent in db seq 1 631
> 1 occurrence(s) of pattern in query
> Name Cyclic nucleotide-binding domain signature 1
> Pattern [LIVM]-[VIC]-x-{H}-G-[DENQTA]-x-[GAC]-{L}-x-[LIVMFY](4)-x(2)-G
> At position 450 of query sequence
> effective database length=3.1e+008
> pattern probability=7.0e-008
> lengthXprobability=2.2e+001
> Number of occurrences of pattern in the database is 247
> 892602 gi|33859524|ref|NP_034048.1|
> 0 Total Score 3279 Outside Pattern Score 3188 Match start in db seq 450
> Extent in query seq 1 631 Extent in db seq 1 631

The input pattern.txt file contains two patterns, so the result contains two sections, one for each pattern. Only one database match is shown.

4.5. seedp

This function is similar to patseedp. The only difference is that the pattern file should specify the pattern position in the input query sequence. The output from the patternp can be used for this purpose. This specifies which pattern is to be used during the search.

An actual command line and pattern file is listed below. Output is omitted since it is essential the same as that from patseedp given above.

> seedtop -p seedp -k pattern2a.txt -d refseq_protein -i q_aa.txt -o seed.out
> ID Cyclic nucleotide-binding domain signature 1
> PA [LIVM]-[VIC]-x-{H}-G-[DENQTA]-x-[GAC]-{L}-x-[LIVMFY](4)-x(2)-G
> HI (450 451) (453 455) (457 458) (460 463) (466 466)

The seedp functionality has been incorporated into standalone blastpgp, on the BLAST web server, it is called Pattern-Hit-Initiated BLAST or PHI-BLAST. The differences are that blastpgp does not report the total number of pattern occurrences in the database, but it does generate actual sequence alignments. The implementation in blastpgp provides more functionality in that the results of the (first) round of PHI-BLAST search can be used seamlessly as the start of a PSI-BLAST iterated search.

4.6. For nucleotide searches
Search for nucleotide patterns using seedtop is very similar to what described above for proteins queries. The function names for nucleotide have no terminating p.
5. Technical Support

For additional questions and comments, please write to:

> blast-help@ncbi.nlm.nih.gov

Questions and inquries on other NCBI resources should be sent to:

> info@ncbi.nlm.nih.gov