Seedtop Document

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
5. Technical Support

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