Ajuda pel Blast


Balast Help Manual

 

DESCRIPTION

 

This document describes the WWW BLAST interface.

 

BLAST (Basic Local Alignment Search Tool) is the heuristic

search algorithm employed by the programs blastp, blastn,

blastx, tblastn, and tblastx; these programs ascribe signi-

ficance to their findings using the statistical methods of

Karlin and Altschul (1990, 1993) with a few enhancements.

The BLAST programs were tailored for sequence similarity

searching -- for example to identify homologs to a query

sequence. The programs are not generally useful for motif-

style searching. For a discussion of basic issues in simi-

larity searching of sequence databases, see Altschul et al.

(1994).

 

The five BLAST programs described here perform the following

tasks:

 

blastp compares an amino acid query sequence against a

protein sequence database;

 

blastn compares a nucleotide query sequence against a

nucleotide sequence database;

 

blastx compares the six-frame conceptual translation

products of a nucleotide query sequence (both

strands) against a protein sequence database;

 

tblastn compares a protein query sequence against a

nucleotide sequence database dynamically

translated in all six reading frames (both

strands).

 

tblastx compares the six-frame translations of a nucleo-

tide query sequence against the six-frame transla-

tions of a nucleotide sequence database.

 

 

BLAST Search parameters

 

HISTOGRAM

Display a histogram of scores for each search; default

is yes. (See parameter H in the BLAST Manual).

DESCRIPTIONS

Restricts the number of short descriptions of matching

sequences reported to the number specified; default

limit is 100 descriptions. (See parameter V in the

manual page). See also EXPECT and CUTOFF.

ALIGNMENTS

Restricts database sequences to the number specified for

which high-scoring segment pairs (HSPs) are reported;

the default limit is 50. If more database sequences

than this happen to satisfy the statistical

significance threshold for reporting (see EXPECT and

CUTOFF below), only the matches ascribed the greatest

statistical significance are reported.

(See parameter B in the BLAST Manual).

EXPECT

 

The statistical significance threshold for reporting

matches against database sequences; the default value

is 10, such that 10 matches are expected to be found

merely by chance, according to the stochastic model

of Karlin and Altschul (1990). If the statistical

significance ascribed to a match is greater than the

EXPECT threshold, the match will not be reported.

Lower EXPECT thresholds are more stringent, leading

to fewer chance matches being reported. Fractional

values are acceptable. (See parameter E in the BLAST

Manual).

CUTOFF

 

Cutoff score for reporting high-scoring segment pairs.

The default value is calculated from the EXPECT value

(see above). HSPs are reported for a database sequence

only if the statistical significance ascribed to them

is at least as high as would be ascribed to a lone

HSP having a score equal to the CUTOFF value. Higher

CUTOFF values are more stringent, leading to fewer

chance matches being reported. (See parameter S in

the BLAST Manual). Typically, significance thresholds

can be more intuitively managed using EXPECT.

MATRIX

 

Specify an alternate scoring matrix for BLASTP, BLASTX,

TBLASTN and TBLASTX. The default matrix is BLOSUM62

(Henikoff & Henikoff, 1992). The valid alternative

choices include: PAM40, PAM120, PAM250 and IDENTITY.

No alternate scoring matrices are available for BLASTN;

specifying the MATRIX directive in BLASTN requests

returns an error response.

STRAND

 

Restrict a TBLASTN search to just the top or bottom

strand of the database sequences; or restrict a BLASTN,

BLASTX or TBLASTX search to just reading frames on the

top or bottom strand of the query sequence.

FILTER

 

Mask off segments of the query sequence that have

low compositional complexity, as determined by the

SEG program of Wootton & Federhen (Computers and

Chemistry, 1993), or segments consisting of

short-periodicity internal repeats, as determined

by the XNU program of Claverie & States (Computers

and Chemistry, 1993), or, for BLASTN, by the DUST

program of Tatusov and Lipman (in preparation).

Filtering can eliminate statistically significant but

biologically uninteresting reports from the blast

output (e.g., hits against common acidic-, basic- or

proline-rich regions), leaving the more biologically

interesting regions of the query sequence available

for specific matching against database sequences.

 

Low complexity sequence found by a filter program is

substituted using the letter "N" in nucleotide sequence

(e.g., "NNNNNNNNNNNNN") and the letter "X" in protein

sequences (e.g., "XXXXXXXXX"). Users may turn off

filtering by using the "Filter" option on the "Advanced

options for the BLAST server" page.

 

Filtering is only applied to the query sequence (or

its translation products), not to database sequences.

Default filtering is DUST for BLASTN, SEG for other

programs.

 

It is not unusual for nothing at all to be masked

by SEG, XNU, or both, when applied to sequences

in SWISS-PROT, so filtering should not be expected to

always yield an effect. Furthermore, in some cases,

sequences are masked in their entirety, indicating that

the statistical significance of any matches reported

against the unfiltered query sequence should be suspect.

 

NCBI-gi

 

Causes NCBI gi identifiers to be shown in the output,

in addition to the accession and/or locus name.

 

 

SEARCH STRATEGY

 

The fundamental unit of BLAST algorithm output is the High-

scoring Segment Pair (HSP). An HSP consists of two sequence

fragments of arbitrary but equal length whose alignment is

locally maximal and for which the alignment score meets or

exceeds a threshold or cutoff score. A set of HSPs is thus

defined by two sequences, a scoring system, and a cutoff

score; this set may be empty if the cutoff score is suffi-

ciently high. In the programmatic implementations of the

BLAST algorithm described here, each HSP consists of a seg-

ment from the query sequence and one from a database

sequence. The sensitivity and speed of the programs can be

adjusted via the standard BLAST algorithm parameters W, T,

and X (Altschul et al., 1990); selectivity of the programs

can be adjusted via the cutoff score.

 

A Maximal-scoring Segment Pair (MSP) is defined by two

sequences and a scoring system and is the highest-scoring of

all possible segment pairs that can be produced from the two

sequences. The statistical methods of Karlin and Altschul

(1990, 1993) are applicable to determining the significance

of MSP scores in the limit of long sequences, under a random

sequence model that assumes independent and identically dis-

tributed choices for the residues at each position in the

sequences. In the programs described here, Karlin-Altschul

statistics have been extrapolated to the task of assessing

the significance of HSP scores obtained from comparisons of

potentially short, biological sequences.

 

The approach to similarity searching taken by the BLAST pro-

grams is first to look for similar segments (HSPs) between

the query sequence and a database sequence, then to evaluate

the statistical significance of any matches that were found,

and finally to report only those matches that satisfy a

user-selectable threshold of significance. Findings of mul-

tiple HSPs involving the query sequence and a single data-

base sequence may be treated statistically in a variety of

ways. By default the programs use "Sum" statistics (Karlin

and Altschul, 1993). As such, the statistical significance

ascribed to a set of HSPs may be higher than that ascribed

to any individual member of the set. Only when the ascribed

significance satisfies the user-selectable threshold (E

parameter) will the match be reported to the user.

 

The task of finding HSPs begins with identifying short words

of length W in the query sequence that either match or

satisfy some positive-valued threshold score T when aligned

with a word of the same length in a database sequence. T is

referred to as the neighborhood word score threshold

(Altschul et al., 1990). These initial neighborhood word

hits act as seeds for initiating searches to find longer

HSPs containing them. The word hits are extended in both

directions along each sequence for as far as the cumulative

alignment score can be increased. Extension of the word

hits in each direction are halted when: the cumulative

alignment score falls off by the quantity X from its maximum

achieved value; the cumulative score goes to zero or below,

due to the accumulation of one or more negative-scoring

residue alignments; or the end of either sequence is

reached.

 

KARLIN-ALTSCHUL STATISTICS

From Karlin and Altschul (1990), the principal equation

relating the score of an HSP to its expected frequency of

chance occurrence is:

 

E = K N exp(-Lambda S)

 

where E is the expected frequency of chance occurrence of an

HSP having score S (or one scoring higher); K and Lambda are

Karlin-Altschul parameters; N is the product of the query

and database sequence lengths, or the size of the search

space; and exp is the exponentiation function.

 

Lambda may be thought of as the expected increase in relia-

bility of an alignment associated with a unit increase in

alignment score. Reliability in this case is expressed in

units of information, such as bits or nats, with one nat

being equivalent to 1/log(2) (roughly 1.44) bits.

 

The expectation E (range 0 to infinity) calculated for an

alignment between the query sequence and a database sequence

can be extrapolated to an expectation over the entire

database search, by converting the pairwise expectation to a

probability (range 0-1) and multiplying the result by the

ratio of the entire database size (expressed in residues) to

the length of the matching database sequence. In detail:

 

E_database = (1 - exp(-E)) D / d

 

where D is the size of the database; d is the length of the

matching database sequence; and the quantity (1 - exp(-E))

is the probability, P, corresponding to the expectation E

for the pairwise sequence comparison. Note that in the

limit of infinite E, P approaches 1; and in the limit as E

approaches 0, E and P approach equality. Due to inaccuracy

in the statistical methods as they are applied in the BLAST

programs, whenever E and P are less than about 0.05, the two

values can be practically treated as being equal.

 

In contrast to the random sequence model used by Karlin-

Altschul statistics, biological sequences are often short in

length -- an HSP may involve a relatively large fraction of

the query or database sequence, which reduces the effective

size of the 2-dimensional search space defined by the two

sequences. To obtain more accurate significance estimates,

the BLAST programs compute effective lengths for the query

and database sequences that are their real lengths minus the

expected length of the HSP, where the expected length for an

HSP is computed from its score. In no event is an effective

length for the query or database sequence permitted to go

below 1. Thus, the effective length of either the query or

the database sequence is computed according to the follow-

ing:

 

Length_eff = MAX( Length_real - Lambda S / H , 1)

 

where H is the relative entropy of the target and background

residue frequencies (Karlin and Altschul, 1990), one of the

statistics reported by the BLAST programs. H may be thought

of as the information expected to be obtained from each pair

of aligned residues in a real alignment that distinguishes

the alignment from a random one.

 

SCORING SCHEMES

 

The default scoring matrix used by blastp, blastx, tblastn,

and tblastx is the BLOSUM62 matrix (Henikoff and Henikoff,

1992).

 

Several PAM (point accepted mutations per 100 residues)

amino acid scoring matrices are provided in the BLAST

software distribution, including the PAM40, PAM120, and

PAM250. While the BLOSUM62 matrix is a good general purpose

scoring matrix and is the default matrix used by the BLAST

programs, if one is restricted to using only PAM scoring

matrices, then the PAM120 is recommended for general protein

similarity searches (Altschul, 1991). The pam(1) program

can be used to produce PAM matrices of any desired iteration

from 2 to 511. Each matrix is most sensitive at finding

similarities at its particular PAM distance. For more

thorough searches, particularly when the mutational distance

between potential homologs is unknown and the significance

of their similarity may be only marginal, Altschul (1991,

1992) recommends performing at least three searches, one

each with the PAM40, PAM120 and PAM250 matrices.

 

In blastn, the M parameter sets the reward score for a pair

of matching residues; the N parameter sets the penalty score

for mismatching residues. M and N must be positive and

negative integers, respectively. The relative magnitudes of

M and N determines the number of nucleic acid PAMs (point

accepted mutations per 100 residues) for which they are most

sensitive at finding homologs. Higher ratios of M:N

correspond to increasing nucleic acid PAMs (increased diver-

gence). The default values for M and N, respectively 5 and

-4, having a ratio of 1.25, correspond to about 47 nucleic

acid PAMs, or about 58 amino acid PAMs; an M:N ratio of 1

corresponds to 30 nucleic acid PAMs or 38 amino acid PAMs.

At higher than about 40 nucleic acid PAMs, or 50 amino acid

PAMs, better sensitivity at detecting similarities between

coding regions is expected by performing comparisons at the

amino acid level (States et al., 1991), using conceptually

translated nucleotide sequences (re: blastx, tblastn, and

tblastx).

 

Independent of the values chosen for M and N, the default

wordlength W=11 used by blastn restricts the program to

finding sequences that share at least an 11-mer stretch of

100% identity with the query. Under the random sequence

model, stretches of 11 consecutive matching residues are

unlikely to occur merely by chance even between only

moderately diverged homologs. Thus, blastn with its default

parameter settings is poorly suited to finding anything but

very similar sequences. If better sensitivity is needed,

one should use a smaller value for W.

 

For the blastn program, it may be easy to see how multiply-

ing both M and N by some large number will yield proportion-

ally larger alignment scores with their statistical signifi-

cance remaining unchanged. This scale-independence of the

statistical significance estimates from blastn has its ana-

log in the scoring matrices used by the other BLAST pro-

grams: multiplying all elements in a scoring matrix by an

arbitrary factor will proportionally alter the alignment

scores but will not alter their statistical significance

(assuming numerical precision is maintained). From this it

should be clear that raw alignment scores are meaningless

without specific knowledge of the scoring matrix that was

used.

 

SCORING REQUIREMENTS

 

Regardless of the scoring scheme employed, two stringent

criteria must be met in order to be able to calculate the

Karlin-Altschul parameters Lambda and K. First, given the

residue composition for the query sequence and the residue

composition assumed for the database, the alignment score

expected for any randomly selected pair of residues (one

from the query sequence and one from the database) must be

negative. Second, given the sequence residue compositions

and the scoring scheme, a positive score must be possible to

achieve. For instance, the match reward score of blastn

must have a positive value; and given the assumption made by

blastn that the 4 nucleotides A, C, G and T are represented

at equal 25% frequencies in the database, a wide range of

value combinations for M and N are precluded from use --

namely those combinations where the magnitude of the ratio

M:N is greater than or equal to 3.

 

 

GENETIC CODES

 

The parameter C can be set to a positive integer to select

the genetic code that will be used by blastx and tblastx to

translate the query sequence. The -dbgcode parameter can be

used to select an alternate genetic code for translation of

the database by the programs tblastn and tblastx. In each

case, the default genetic code is the so-called "Standard"

or "Universal" genetic code. To obtain a listing of the

genetic codes available and their associated numerical iden-

tifiers, invoke blastx or tblastx with the command line

parameter C=list. Note: the numerical identifiers used here

for genetic codes parallel those defined in the NCBI

software Toolbox; hence some numerical values will be

skipped as genetic codes are updated.

 

The list of genetic codes available and their associated

values for the parameters C and -dbgcode are:

 

1 Standard or Universal

 

2 Vertebrate Mitochondrial

 

3 Yeast Mitochondrial

 

4 Mold, Protozoan, Coelenterate Mitochondrial and

Mycoplasma/Spiroplasma

 

5 Invertebrate Mitochondrial

 

6 Ciliate Macronuclear

 

9 Echinodermate Mitochondrial

 

10 Alternative Ciliate Macronuclear

 

11 Eubacterial

 

12 Alternative Yeast

 

13 Ascidian Mitochondrial

 

14 Flatworm Mitochondrial

 

 

P-VALUES, ALIGNMENT SCORES, AND INFORMATION

 

The Expect and P-values reported for HSPs are dependent on

several factors including: the scoring system employed, the

residue composition of the query sequence, an assumed resi-

due composition for a typical database sequence, the length

of the query sequence, and the total length of the database.

HSP scores from different program invocations are appropri-

ate for comparison even if the databases searched are of

different lengths, as long as the other factors mentioned

here do not vary. For example, alignment scores from

searches with the default BLOSUM62 matrix should not be

directly compared with scores obtained with the PAM120

matrix; and scores produced using two versions of the same

PAM matrix, each created to different scales (see above),

can not be meaningfully compared without conversion to the

same scale.

 

Some isolation from the many factors involved in assessing

the statistical significance of HSPs can be attained by

observing the information content reported (in bits) for the

alignments. While the information content of an HSP may

change when different scoring systems are used (e.g., with

different PAM matrices), the number of bits reported for an

HSP will at least be independent of the scale to which the

scoring matrix was generated. (In practice, this statement

is not quite true, because the alignment scores used by the

BLAST programs are integers that lack much precision). In

other words, when conveying the statistical significance of

an alignment, the alignment score itself is not useful

unless the specific scoring matrix that was employed is also

provided, but the informativeness of an alignment is a mean-

ingful statistic that can be used to ascribe statistical

significance (a P-value) to the match independently of

specific knowledge about the scoring matrix.

 

SAMPLE OUTPUT

 

The BLAST programs all provide information in roughly the

same format. First comes (A) an introduction to the pro-

gram; (B) a histogram of expectations (see above) if one was

requested; (C) a series of one-line descriptions of matching

database sequences; (D) the actual sequence alignments; and

finally the parameters and other statistics gathered during

the search.

 

Sample blastp output from comparing pir|A01243|DXCH against

the SWISS-PROT database is presented below.

 

A. Program Introduction

The introductory output provides the program name (BLASTP in

this case), the version number (1.4.6MP in this case), the

date the program source code last changed substantially

(June 13, 1994), the date the program was built (Sept. 22,

1994), and a description of the query sequence and database

to be searched. These may all be important pieces of infor-

mation if a bug is suspected or if reproducibility of

results is important.

 

The "Searching..." indicator indicates progress that the

program made in searching the database. A complete database

search will yield 50 periods (.), or one period per database

sequence, whichever number is smaller. When searching a

database consisting of 50 sequences or more, if fewer than

50 periods are displayed and the program aborted for some

reason, dividing the number of periods by 0.5 will yield the

approximate percentage (0-100%) of the database that was

searched before the program died. If the program had diffi-

culty making progress through the database, one or more

asterisks (*) may be interspersed between the periods at

one-minute intervals.

 

B. Histogram of Expectations

Shown in the output below is a histogram of the lowest (most

significant) Expect values obtained with each database

sequence. This information is useful in determining the

numbers of database sequences that achieved a particular

level of statistical significance. It indicates the number

of database matches that would be reportable at various set-

tings for the expectation threshold (E parameter).

 

C. One-line Summaries

The one-line sequence descriptions and summaries of results

are useful for identifying biologically interesting database

matches and correlating this interest with the statistical

significance estimates. Unless otherwise requested, the

database sequences are sorted by increasing P-value (proba-

bility). Identifiers for the database sequences appear in

the first column; then come brief descriptions of each

sequence, which may need to be truncated in order to fit in

the available space. The "High Score" column contains the

score of the highest-scoring HSP found with each database

sequence. The "P(N)" column contains the lowest P-value

ascribed to any set of HSPs for each database sequence; and

the "N" column displays the number of HSPs in the set which

was ascribed the lowest P-value. The P-values are a func-

tion of N, as used in Karlin-Altschul "Sum" statistics or

Poisson statistics, to treat situations where multiple HSPs

are found. It should be noted that the highest-scoring HSP

whose score is reported in the "High Score" column is not

necessarily a member of the set of HSPs which yields the

lowest P-value; the highest-scoring HSP may be excluded from

this set on the basis of consistency rules governing the

grouping of HSPs (see the -consistency option). Numbers of

the form "7.7e-160" are in scientific notation. In this

particular example, the number being represented is 7.7

times 10 to the minus 160th power. which is astronomically

close to zero.

 

D. Alignments

Alignments found with the BLAST algorithm are ungapped.

Several statistics are used to describe each HSP: the raw

alignment Score; the raw score converted to bits of informa-

tion by multiplying by Lambda (see the Statistics output);

the number of times one might Expect to see such a match (or

a better one) merely by chance; the P-value (probability in

the range 0-1) of observing such a match; the number and

fraction of total residues in the HSP which are identical;

the number and fraction of residues for which the alignment

scores have positive values. When Sum statistics have been

used to calculate the Expect and P-values, the P-value is

qualified with the word "Sum" and the N parameter used in

the Sum statistics is provided in parentheses to indicate

the number of HSPs in the set; when Poisson statistics have

been used to calculate the Expect and P-values, the P-value

is qualified with the word "Poisson". Between the two lines

of Query and Subject (database) sequence is a line indicat-

ing the specific residues which are identical, as well as

those which are non-identical but nevertheless have positive

alignment scores defined in the scoring matrix that was used

(the BLOSUM62 matrix in this case). Identical letters or

residues, when paired with each other, are not highlighted

if their alignment score is negative or zero. Examples of

this would be an X juxtaposed with an X in two amino acid

sequences, or an N juxtaposed with another N in two nucleo-

tide sequences. Such ambiguous residue-residue pairings may

be uninformative and thus lend no support to the overall

alignment being either real or random; however, the informa-

tiveness of these pairings is left up to the user of the

BLAST programs to decide, because any values desired can be

specified in a scoring matrix of the user's own making.

 

BLASTP 1.4.6MP [13-Jun-94] [Build 13:58:36 Sep 22 1994]

 

Reference: Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers,

and David J. Lipman (1990). Basic local alignment search tool. J. Mol. Biol.

215:403-10.

 

Query = pir|A01243|DXCH 232 Gene X protein - Chicken (fragment)

(232 letters)

 

Database: SWISS-PROT Release 29.0

38,303 sequences; 13,464,008 total letters.

Searching..................................................done

 

 

Observed Numbers of Database Sequences Satisfying

Various EXPECTation Thresholds (E parameter values)

 

Histogram units: = 31 Sequences : less than 31 sequences

 

EXPECTation Threshold

(E parameter)

|

V Observed Counts-->

10000 4863 1861 |============================================================

6310 3002 782 |=========================

3980 2220 812 |==========================

2510 1408 303 |=========

1580 1105 393 |============

1000 712 179 |=====

631 533 161 |=====

398 372 80 |==

251 292 73 |==

158 219 50 |=

100 169 32 |=

63.1 137 18 |:

39.8 119 9 |:

25.1 110 6 |:

15.8 104 9 |:

>>>>>>>>>>>>>>>>>>>>> Expect = 10.0, Observed = 95 <<<<<<<<<<<<<<<<<

10.0 95 4 |:

6.31 91 3 |:

3.98 88 1 |:

2.51 87 3 |:

1.58 84 0 |

1.00 84 2 |:

 

 

Smallest

Sum

High Probability

Sequences producing High-scoring Segment Pairs: Score P(N) N

 

sp|P01013|OVAX_CHICK GENE X PROTEIN (OVALBUMIN-RELATED) (... 1191 7.7e-160 1

sp|P01014|OVAY_CHICK GENE Y PROTEIN (OVALBUMIN-RELATED). 949 7.0e-127 1

sp|P01012|OVAL_CHICK OVALBUMIN (PLAKALBUMIN). 645 3.4e-100 2

sp|P19104|OVAL_COTJA OVALBUMIN. 626 1.2e-96 2

sp|P05619|ILEU_HORSE LEUKOCYTE ELASTASE INHIBITOR (LEI). 216 3.7e-71 3

sp|P80229|ILEU_PIG LEUKOCYTE ELASTASE INHIBITOR (LEI) (... 325 4.0e-71 2

sp|P29508|SCCA_HUMAN SQUAMOUS CELL CARCINOMA ANTIGEN (SCC... 439 3.5e-70 2

sp|P30740|ILEU_HUMAN LEUKOCYTE ELASTASE INHIBITOR (LEI) (... 211 1.3e-66 3

sp|P05120|PAI2_HUMAN PLASMINOGEN ACTIVATOR INHIBITOR-2, P... 176 1.8e-65 4

sp|P35237|PTI_HUMAN PLACENTAL THROMBIN INHIBITOR. 473 1.3e-61 1

sp|P29524|PAI2_RAT PLASMINOGEN ACTIVATOR INHIBITOR-2, T... 183 9.4e-61 4

sp|P12388|PAI2_MOUSE PLASMINOGEN ACTIVATOR INHIBITOR-2, M... 179 1.8e-60 4

sp|P36952|MASP_HUMAN MASPIN PRECURSOR. 198 2.6e-58 4

sp|P32261|ANT3_MOUSE ANTITHROMBIN-III PRECURSOR (ATIII). 142 4.0e-48 5

sp|P01008|ANT3_HUMAN ANTITHROMBIN-III PRECURSOR (ATIII). 122 7.5e-48 5

 

WARNING: Descriptions of 80 database sequences were not reported due to the

limiting value of parameter V = 15.

 

 

... alignments with the top 8 database sequences deleted ...

 

>sp|P05120|PAI2_HUMAN PLASMINOGEN ACTIVATOR INHIBITOR-2, PLACENTAL (PAI-2)

(MONOCYTE ARG- SERPIN).

Length = 415

 

Score = 176 (80.2 bits), Expect = 1.8e-65, Sum P(4) = 1.8e-65

Identities = 38/89 (42%), Positives = 50/89 (56%)

 

Query: 1 QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNN 60

+I +LL S D DT +VLVNA+YFKG WKT F + PF V + PVQMM +

Sbjct: 180 KIPNLLPEGSVDGDTRMVLVNAVYFKGKWKTPFEKKLNGLYPFRVNSAQRTPVQMMYLRE 239

 

Query: 61 SFNVATLPAEKMKILELPFASGDLSMLVL 89

N+ + K +ILELP+A L+L

Sbjct: 240 KLNIGYIEDLKAQILELPYAGDVSMFLLL 268

 

Score = 165 (75.2 bits), Expect = 1.8e-65, Sum P(4) = 1.8e-65

Identities = 33/78 (42%), Positives = 47/78 (60%)

 

Query: 155 ANLTGISSAESLKISQAVHGAFMELSEDGIEMAGSTGVIEDIKHSPESEQFRADHPFLFL 214

AN +G+S L +S+ H A ++++E+G E A TG + + QF ADHPFLFL

Sbjct: 338 ANFSGMSERNDLFLSEVFHQAMVDVNEEGTEAAAGTGGVMTGRTGHGGPQFVADHPFLFL 397

 

Query: 215 IKHNPTNTIVYFGRYWSP 232

I H T I++FGR+ SP

Sbjct: 398 IMHKITKCILFFGRFCSP 415

 

Score = 144 (65.6 bits), Expect = 1.8e-65, Sum P(4) = 1.8e-65

Identities = 26/62 (41%), Positives = 41/62 (66%)

 

Query: 90 LPDEVSDLERIEKTINFEKLTEWTNPNTMEKRRVKVYLPQMKIEEKYNLTSVLMALGMTD 149

+ D + LE +E I ++KL +WT+ + M + V+VY+PQ K+EE Y L S+L ++GM D

Sbjct: 272 IADVSTGLELLESEITYDKLNKWTSKDKMAEDEVEVYIPQFKLEEHYELRSILRSMGMED 331

 

Query: 150 LF 151

F

Sbjct: 332 AF 333

 

Score = 61 (27.8 bits), Expect = 1.8e-65, Sum P(4) = 1.8e-65

Identities = 10/17 (58%), Positives = 16/17 (94%)

 

Query: 81 SGDLSMLVLLPDEVSDL 97

+GD+SM +LLPDE++D+

Sbjct: 259 AGDVSMFLLLPDEIADV 275

 

 

WARNING: HSPs involving 86 database sequences were not reported due to the

limiting value of parameter B = 9.

 

 

Parameters:

V=15

B=9

H=1

 

-ctxfactor=1.00

E=10

 

Query ----- As Used ----- ----- Computed ----

Frame MatID Matrix name Lambda K H Lambda K H

+0 0 BLOSUM62 0.316 0.132 0.370 same same same

 

Query

Frame MatID Length Eff.Length E S W T X E2 S2

+0 0 232 232 10. 57 3 11 22 0.22 33

 

 

Statistics:

Query Expected Observed HSPs HSPs

Frame MatID High Score High Score Reportable Reported

+0 0 62 (28.2 bits) 1191 (542.5 bits) 330 24

 

Query Neighborhd Word Excluded Failed Successful Overlaps

Frame MatID Words Hits Hits Extensions Extensions Excluded

+0 0 4988 5661199 1146395 4504598 10187 13

 

Database: SWISS-PROT Release 29.0

Release date: June 1994

Posted date: 1:29 PM EDT Jul 28, 1994

# of letters in database: 13,464,008

# of sequences in database: 38,303

# of database sequences satisfying E: 95

No. of states in DFA: 561 (55 KB)

Total size of DFA: 110 KB (128 KB)

Time to generate neighborhood: 0.03u 0.01s 0.04t Real: 00:00:00

No. of processors used: 8

Time to search database: 32.27u 0.78s 33.05t Real: 00:00:04

Total cpu time: 32.33u 0.91s 33.24t Real: 00:00:05

 

WARNINGS ISSUED: 2

 

COPYRIGHT

This work is in the public domain.

REFERENCES

Altschul, Stephen F. (1991). Amino acid substitution

matrices from an information theoretic perspective. J. Mol.

Biol. 219:555-65.

 

Altschul, S. F. (1993). A protein alignment scoring system

sensitive at all evolutionary distances. J. Mol. Evol.

36:290-300.

 

Altschul, S. F., M. S. Boguski, W. Gish and J. C. Wootton

(1994). Issues in searching molecular sequence databases.

Nature Genetics 6:119-129.

 

Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W.

Myers, and David J. Lipman (1990). Basic local alignment

search tool. J. Mol. Biol. 215:403-10.

 

Claverie, J.-M. and D. J. States (1993). Information

enhancement methods for large scale sequence analysis. Com-

puters in Chemistry 17:191-201.

 

Gish, W. and D. J. States (1993). Identification of protein

coding regions by database similarity search. Nature Genet-

ics 3:266-72.

 

Henikoff, Steven and Jorga G. Henikoff (1992). Amino acid

substitution matrices from protein blocks. Proc. Natl. Acad.

Sci. USA 89:10915-19.

 

Karlin, Samuel and Stephen F. Altschul (1990). Methods for

assessing the statistical significance of molecular sequence

features by using general scoring schemes. Proc. Natl. Acad.

Sci. USA 87:2264-68.

 

Karlin, Samuel and Stephen F. Altschul (1993). Applications

and statistics for multiple high-scoring segments in molecu-

lar sequences. Proc. Natl. Acad. Sci. USA 90:5873-7.

 

States, D. J. and W. Gish (1994). Combined use of sequence

similarity and codon bias for coding region identification.

J. Comput. Biol. 1:39-50.

 

States, D. J., W. Gish and S. F. Altschul (1991). Improved

sensitivity of nucleic acid database similarity searches

using application specific scoring matrices. Methods: A com-

panion to Methods in Enzymology 3:66-70.

 

Wootton, J. C. and S. Federhen (1993). Statistics of local

complexity in amino acid sequences and sequence databases.

Computers in Chemistry 17:149-163.


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