_scan_database_report (
        self,
        uhandle,
        consumer,
        )

Database: sdqib40-1.35.seg.fa Posted date: Nov 1, 1999 4:25 PM Number of letters in database: 223,339 Number of sequences in database: 1323

Lambda K H

Gapped Lambda K H

_scan_descriptions (
        self,
        uhandle,
        consumer,
        )

Searching..................................................done Results from round 2

Sc Sequences producing significant alignments: (b Sequences used in model and found again:

d1tde2 3.4.1.4.4 (119-244) Thioredoxin reductase [Escherichia ... d1tcob 1.31.1.5.16 Calcineurin regulatory subunit (B-chain) [B... d1symb_ 1.31.1.2.2 Calcyclin (S100) [RAT (RATTUS NORVEGICUS)]

Sequences not found previously or not previously below threshold:

d1osa__ 1.31.1.5.11 Calmodulin [Paramecium tetraurelia] d1aoza3 2.5.1.3.3 (339-552) Ascorbate oxidase [zucchini (Cucurb...

_scan_header (
        self,
        uhandle,
        consumer,
        )

BLASTP 2.0.10 [Aug-26-1999]

Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaf Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database sea programs", Nucleic Acids Res. 25:3389-3402.

Query= test (140 letters)

Database: sdqib40-1.35.seg.fa 1323 sequences; 223,339 total letters

_scan_hsp_alignment (
        self,
        uhandle,
        consumer,
        )

Query: 11 GRGVSACA-------TCDGFFYRNQKVAVIGGGNTAVEEALYLSNIASEVHLIHRRDGF GRGVS+ TC Y + + V GGG+ + EE L + I R+ Sbjct: 12 GRGVSSVVRRCIHKPTCKE--YAVKIIDVTGGGSFSAEEVQELREATLKEVDILRKVSG

Query: 64 AEKILIKR 71 I +K Sbjct: 70 PNIIQLKD 77

_scan_hsp_header (
        self,
        uhandle,
        consumer,
        )

Score = 22.7 bits (47), Expect = 2.5 Identities = 10/36 (27%), Positives = 18/36 (49%) Strand = Plus / Plus Frame = +3

_scan_parameters (
        self,
        uhandle,
        consumer,
        )

Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 50604 Number of Sequences: 1323 Number of extensions: 1526 Number of successful extensions: 6 Number of sequences better than 10.0: 5 Number of HSP's better than 10.0 without gapping: 5 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 1 Number of HSP's gapped (non-prelim): 5 length of query: 140 length of database: 223,339 effective HSP length: 39 effective length of query: 101 effective length of database: 171,742 effective search space: 17345942 effective search space used: 17345942 T: 11 A: 40 X1: 16 ( 7.4 bits) X2: 38 (14.8 bits) X3: 64 (24.9 bits) S1: 41 (21.9 bits) S2: 42 (20.8 bits)

_scan_rounds (
        self,
        uhandle,
        consumer,
        )

Scan a bunch of rounds. Each round begins with either a "Searching......" line or a Score E line followed by descriptions and alignments. The email server doesn't give the "Searching....." line.

feed (
        self,
        handle,
        consumer,
        )

1. feed(handle, consumer)

   Feed in a BLAST report for scanning. handle is a file-like object that contains the BLAST report. consumer is a Consumer object that will receive events as the report is scanned.