ncbi fieldguide a field guide part 2 august 30, 2005 university of colorado health sciences center

eA Field Guide part 2

August 30, 2005 University of Colorado Health Sciences Center

ePart 2

Entrez: text searching• a GenBank record• preview/index

BLAST: sequence searching• pre-computed searches• algorithms• what’s new?

VAST: structure searching

Example: mapping oligos to a genome

eGenBank Records

Header

Feature Table

Sequence

The Flatfile Format

eA Typical GenBank Record

LOCUS NM_019570 4279 bp mRNA linear INV 28-OCT-2004DEFINITION Mus musculus REV1-like(S. cerevisiae)(Rev1l),mRNAACCESSION NM_019570VERSION NM_019570.3 GI:50811869 KEYWORDS .

= Title

eGenBank Record: Feature Table

GenPept identifier

GenBank Record: Feature Table, con’t.

eGenBank Record: sequence

eIndexing for Nucleotide UID 59958365

Field Indexed Terms

[primary accession] NM_001012399[title] Bos taurus hemochromatosis (hfe), mRNA.[organism] Bos taurus[sequence length] 1168[modification date] 2005/02/19[properties] biomol mrna

gbdiv mamsrcdb refseq

[accn]

[orgn]

[mdat][prop]

eGlobal Entrez Search: HFE

Entrez Nucleotide: HFE 137 records

Not HFE [Title]

eSmarter Query

hfe[title]

42 records

Curated HFE splice variants(11 total)

AND human[orgn]

ehfe[title] AND human[orgn] (con’t)

Primary data

ePreview/Index

ePreview/Index: Properties, srcdb

srcdbProperties

…AND srcdb refseq[Properties]…AND srcdb refseq[Properties]

…AND srcdb ddbj/embl/genbank[Properties]…AND srcdb ddbj/embl/genbank[Properties]

e#1 hfe 137#2 hfe[title] AND human[orgn] 42

#3 #2 AND srcdb refseq[prop] 11#4 #2 AND srcdb ddbj/embl/genbank[prop] 31

Database Queries

#5 #4 AND gbdiv pri[prop] 29

#4 #4 AND gbdiv est[prop] 2

Primate division gbdiv pri[prop]EST division gbdiv est[prop]

Molecule Queries

#1 hfe 116

#2 hfe[title] AND human[orgn] 42

#3 #2 AND biomol mrna[prop] 29

#4 #2 AND biomol genomic[prop] 13

Genomic DNA biomol genomic[prop]cDNA biomol mrna[prop]

eMore Queries…

Fields are database-specific

Entrez Nucleotide

Reviewed RefSeqs with transcript variants:

srcdb refseq reviewed[prop] AND transcript[title] AND variant[title]

Topoisomerase genes from Archaea:

topoisomerase[gene name] AND archaea[organism]

Entrez Gene

Genes on human chromosome 2 with OMIM links

2[chromosome] AND human[organism] AND “gene omim”[filter]

Membrane proteins linked to cancer:

“integral to plasma membrane”[gene ontology] AND cancer[dis]

Other Entrez Databases

UniSTS: markers on the Genethon map of human chromosome 12

Genethon[Map Name] AND human[organism] AND 12[chromosome]

UniGene: rat clusters that have at least one mRNA

rat[organism] NOT 0[mrna count]

Structure: structures of bacterial kinases with resolutions below 2 Å

bacteria[organism] AND kinase AND 000.00:002.00[resolution]

SNP: uniquely mapped microsatellites on human chr2

microsat[SNP Class] AND 1[Map Weight] AND 2[Chromosome]) AND human[orgn]

Basic Local Alignment Search Tool

eBLAST Web Searches, 2005

200,000

Nucleotide or protein: Related

Sequences

BLAST link: BLink

Precomputed BLAST Services

Transcript clusters: UniGene

Protein homologs: HomoloGene

eLink to Related Sequences

eRelated Sequences

Most similar

Least similar

BLink (BLAST Link)

eBLink Output

Best hitsBest hits 3D structures3D structures CDD-SearchCDD-Search

eGlobal vs Local Alignment

Global alignment

Local alignment

Global vs Local Alignment

Seq1: WHEREISWALTERNOW (16aa)Seq2: HEWASHEREBUTNOWISHERE (21aa)

Global

Seq1: 1 W--HEREISWALTERNOW 16 W HERE

Seq2: 1 HEWASHEREBUTNOWISHERE 21

LocalSeq1: 1 W--HERE 5 Seq1: 1 W--HERE 5 W HERE W HERESeq2: 3 WASHERE 9 Seq2: 15 WISHERE 21

eThe Flavors of BLAST

• Standard BLAST– nucleotide, protein and translations (blastn, blastp,

blastx, tblastn, tblastx)– traditional “contiguous” word hit

• Megablast– optimized for large batch searches– can use discontiguous words

• PSI-BLAST– constructs PSSMs automatically; uses as query– very sensitive protein search

• RPS BLAST– searches a database of PSSMs– tool for conserved domain searches

“contiguous”

discontiguous

eFast- heuristic approach based on Smith Waterman

Local alignments

Statistical significance- Expect value

Versatile- blastn, blastp, blastx, tblastn, tblastx, rps-blast,

psi-blast- www, standalone, and network clients

Why Is BLAST So Popular?

How BLAST Works

• Make lookup table of “words” for query

• Scan database for hits

• Ungapped extensions of hits (initial HSPs)

• Gapped extensions (no traceback)

• Gapped extensions (traceback; alignment

details)

• Make lookup table of “words” for query

• Scan database for hits

• Ungapped extensions of hits (initial HSPs)

• Gapped extensions (no traceback)

• Gapped extensions (traceback; alignment

details)

eNucleotide Words

GTACTGGACATGGACCCTACAGGAAQuery:

GTACTGGACAT

TACTGGACATG

ACTGGACATGG

CTGGACATGGA

TGGACATGGAC

GGACATGGACC

GACATGGACCC

ACATGGACCCT

Make a lookuptable of words

11-mer

eProtein Words

GTQITVEDLFYNIATRRKALKNQuery:

Neighborhood Words

LTV, MTV, ISV, LSV, etc.

Make a lookuptable of words

Word size = 3 (default)

Word size can only be 2 or 3

[ -f 11 = blastp default ]

Minimum Requirements for a Hit

• Nucleotide BLAST requires one exact match• Protein BLAST requires two neighboring matches within 40 aa

GTQITVEDLFYNI

SEI YYN

ATCGCCATGCTTAATTGGGCTT

CATGCTTAATT

neighborhood words

one exact match

two matches

[ -A 40 = blastp default ]

BLASTP Summary

YLS HFLSbjct 287 LEETYAKYLHKGASYFVYLSLNMSPEQLDVNVHPSKRIVHFLYDQEI 333

Query 1 IETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESI 47

Gapped extension with trace back

Query 1 IETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESI-LEV… 50 +E YA YL K F+YLSL +SP+ +DVNVHP+K VHFL+++ I + +Sbjct 287 LEETYAKYLHKGASYFVYLSLNMSPEQLDVNVHPSKRIVHFLYDQEIATSI… 337

Final HSP

+E YA YL K F+ L +SP+ +DVNVHP+K V +++ I

High-scoring pair (HSP)

HFL 18HFV 15 HFS 14HWL 13NFL 13DFL 12HWV 10etc …

YLS 15YLT 12 YVS 12YIT 10etc …

Neighborhood words

Neighborhood score threshold

T (-f) =11

Query: IETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESILEV…

example query words

Scoring Systems - Nucleotides

A G C T

A +1 –3 –3 -3

G –3 +1 –3 -3

C –3 –3 +1 -3

T –3 –3 –3 +1

Identity matrix

CAGGTAGCAAGCTTGCATGTCA

|| |||||||||||| ||||| raw score = 19-9 = 10

CACGTAGCAAGCTTG-GTGTCA

[ -r 1 -q -3 ]

eScoring Systems - Proteins

Position Independent MatricesPAM Matrices (Percent Accepted Mutation)

• Derived from observation; small dataset of alignments• Implicit model of evolution• All calculated from PAM1• PAM250 widely used

BLOSUM Matrices (BLOck SUbstitution Matrices)• Derived from observation; large dataset of highly

conserved blocks• Each matrix derived separately from blocks with a

defined percent identity cutoff• BLOSUM62 - default matrix for BLAST

Position Specific Score Matrices (PSSMs)PSI- and RPS-BLAST

A 4R -1 5 N -2 0 6D -2 -2 1 6C 0 -3 -3 -3 9Q -1 1 0 0 -3 5E -1 0 0 2 -4 2 5G 0 -2 0 -1 -3 -2 -2 6H -2 0 1 -1 -3 0 0 -2 8I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 A R N D C Q E G H I L K M F P S T W Y V X

BLOSUM62

Negative for less likely substitutions

FPositive for more likely substitutions

Position-Specific Score Matrix

Serine/Threonine protein kinases catalytic loop

1 7 4PSSM scores 5 4

A R N D C Q E G H I L K M F P S T W Y V 435 K -1 0 0 -1 -2 3 0 3 0 -2 -2 1 -1 -1 -1 -1 -1 -1 -1 -2 436 E 0 1 0 2 -1 0 2 -1 0 -1 -1 0 0 0 -1 0 0 -1 -1 -1 437 S 0 0 -1 0 1 1 0 1 1 0 -1 0 0 0 2 0 -1 -1 0 -1 438 N -1 0 -1 -1 1 0 -1 3 3 -1 -1 1 -1 0 0 -1 -1 1 1 -1 439 K -2 1 1 -1 -2 0 -1 -2 -2 -1 -2 5 1 -2 -2 -1 -1 -2 -2 -1 440 P -2 -2 -2 -2 -3 -2 -2 -2 -2 -1 -2 -1 0 -3 7 -1 -2 -3 -1 -1 441 A 3 -2 1 -2 0 -1 0 1 -2 -2 -2 0 -1 -2 3 1 0 -3 -3 0 442 M -3 -4 -4 -4 -3 -4 -4 -5 -4 7 0 -4 1 0 -4 -4 -2 -4 -1 2 443 A 4 -4 -4 -4 0 -4 -4 -3 -4 4 -1 -4 -2 -3 -4 -1 -2 -4 -3 4 444 H -4 -2 -1 -3 -5 -2 -2 -4 10 -6 -5 -3 -4 -3 -2 -3 -4 -5 0 -5 445 R -4 8 -3 -4 0 -1 -2 -3 -2 -5 -4 0 -3 -2 -4 -3 -3 0 -4 -5 446 D -4 -4 -1 8 -6 -2 0 -3 -3 -5 -6 -3 -5 -6 -4 -2 -3 -7 -5 -5 447 I -4 -5 -6 -6 -3 -4 -5 -6 -5 3 5 -5 1 1 -5 -5 -3 -4 -3 1 448 K 0 0 1 -3 -5 -1 -1 -3 -3 -5 -5 7 -4 -5 -3 -1 -2 -5 -4 -4 449 S 0 -3 -2 -3 0 -2 -2 -3 -3 -4 -4 -2 -4 -5 2 6 2 -5 -4 -4 450 K 0 3 0 1 -5 0 0 -4 -1 -4 -3 4 -3 -2 2 1 -1 -5 -4 -4 451 N -4 -3 8 -1 -5 -2 -2 -3 -1 -6 -6 -2 -4 -5 -4 -1 -2 -6 -4 -5 452 I -3 -5 -5 -6 0 -5 -5 -6 -5 6 2 -5 2 -2 -5 -4 -3 -5 -3 3 453 M -4 -4 -6 -6 -3 -4 -5 -6 -5 0 6 -5 1 0 -5 -4 -3 -4 -3 0 454 V -3 -3 -5 -6 -3 -4 -5 -6 -5 3 3 -4 2 -2 -5 -4 -3 -5 -3 5 455 K -2 1 1 4 -5 0 -1 -2 1 -4 -2 4 -3 -2 -3 0 -1 -5 -2 -3 456 N 1 1 3 0 -4 -1 1 0 -3 -4 -4 3 -2 -5 -2 2 -2 -5 -4 -4 457 D -3 -2 5 5 -1 -1 1 -1 0 -5 -4 0 -2 -5 -1 0 -2 -6 -4 -5 458 L -3 -1 0 -3 0 -3 -2 3 -4 -2 3 0 1 1 -2 -2 -3 5 -1 -3

Position-Specific Score Matrix

catalytic loop

eLocal Alignment Statistics

High scores of local alignments between two random sequencesfollow the Extreme Value Distribution

Score (S)

(applies to ungapped alignments)

E = Kmne-S or E = mn2-S’

K = scale for search space = scale for scoring system S’ = bitscore = (S - lnK)/ln2

Expect ValueE = number of database hits you expect to find by chance, ≥ S

your score

expected number of

random hits

More info: www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html

Gapped Alignments

Gapping provides more biologically realistic alignments

Gapped BLAST parameters are simulated for each scoring matrix

Affine gap costs = -(a+bk)a = gap open penalty b = gap extend penaltyA gap of length 1 receives the score -(a+b)

An Alignment BLAST Cannot Make

1 GAATATATGAAGACCAAGATTGCAGTCCTGCTGGCCTGAACCACGCTATTCTTGCTGTTG || | || || || | || || || || | ||| |||||| | | || | ||| | 1 GAGTGTACGATGAGCCCGAGTGTAGCAGTGAAGATCTGGACCACGGTGTACTCGTTGTCG

61 GTTACGGAACCGAGAATGGTAAAGACTACTGGATCATTAAGAACTCCTGGGGAGCCAGTT | || || || ||| || | |||||| || | |||||| ||||| | | 61 GCTATGGTGTTAAGGGTGGGAAGAAGTACTGGCTCGTCAAGAACAGCTGGGCTGAATCCT

121 GGGGTGAACAAGGTTATTTCAGGCTTGCTCGTGGTAAAAAC |||| || ||||| || || | | |||| || ||| 121 GGGGAGACCAAGGCTACATCCTTATGTCCCGTGACAACAAC

1 GAATATATGAAGACCAAGATTGCAGTCCTGCTGGCCTGAACCACGCTATTCTTGCTGTTG || | || || || | || || || || | ||| |||||| | | || | ||| | 1 GAGTGTACGATGAGCCCGAGTGTAGCAGTGAAGATCTGGACCACGGTGTACTCGTTGTCG

61 GTTACGGAACCGAGAATGGTAAAGACTACTGGATCATTAAGAACTCCTGGGGAGCCAGTT | || || || ||| || | |||||| || | |||||| ||||| | | 61 GCTATGGTGTTAAGGGTGGGAAGAAGTACTGGCTCGTCAAGAACAGCTGGGCTGAATCCT

121 GGGGTGAACAAGGTTATTTCAGGCTTGCTCGTGGTAAAAAC |||| || ||||| || || | | |||| || ||| 121 GGGGAGACCAAGGCTACATCCTTATGTCCCGTGACAACAAC

Reason:

no contiguous exact match of 7 bp.

BLAST 2 Sequences (blastx) output:

An Alignment BLAST Can Make

Solution: compare protein sequences; BLASTXScore = 290 bits (741), Expect = 7e-77Identities = 147/331 (44%), Positives = 206/331 (61%), Gaps = 8/331 (2%)Frame = +3

Score = 290 bits (741), Expect = 7e-77Identities = 147/331 (44%), Positives = 206/331 (61%), Gaps = 8/331 (2%)Frame = +3

Other BLAST Algorithms

• Megablast

• Discontiguous Megablast

• PSI-BLAST

• PHI-BLAST

• Megablast

• Discontiguous Megablast

• PSI-BLAST

• PHI-BLAST

Megablast: NCBI’s Genome Annotator

• Long alignments of similar DNA sequences

• Greedy algorithm

• Concatenation of query sequences

• Faster than blastn; less sensitive

• Long alignments of similar DNA sequences

• Greedy algorithm

• Concatenation of query sequences

• Faster than blastn; less sensitive

MegaBLAST & Word Size

Trade-off: sensitivity vs speed

Too fast foryou?

MegaBLAST & Word Size

Trade-off: sensitivity vs speed

23blastp

828megablast

711blastn

minimumdefaultWORD SIZE

Discontiguous Megablast

• Uses discontiguous word matches

• Better for cross-species comparisons

• Uses discontiguous word matches

• Better for cross-species comparisons

Templates for Discontiguous Words

W = 11, t = 16, coding: 1101101101101101W = 11, t = 16, non-coding: 1110010110110111W = 12, t = 16, coding: 1111101101101101W = 12, t = 16, non-coding: 1110110110110111W = 11, t = 18, coding: 101101100101101101W = 11, t = 18, non-coding: 111010010110010111W = 12, t = 18, coding: 101101101101101101W = 12, t = 18, non-coding: 111010110010110111W = 11, t = 21, coding: 100101100101100101101W = 11, t = 21, non-coding: 111010010100010010111W = 12, t = 21, coding: 100101101101100101101W = 12, t = 21, non-coding: 111010010110010010111

Reference: Ma, B, Tromp, J, Li, M. PatternHunter: faster and more sensitive homology search. Bioinformatics March, 2002; 18(3):440-5

W = word size; # matches in template

t = template length

eDiscontiguous (Cross-species)

MegaBLAST

eDiscontiguous Word

Options

eMegaBLAST vs Discontiguous

MegaBLAST

NM_017460 Homo sapiens cytochrome P450, family 3, subfamily A, polypeptide 4 (CYP3A4),

transcript variant 1, mRNA (2768 letters)

vs Drosophila

MegaBLAST vs Discontiguous MegaBLAST

MegaBLAST = “No significant similarity found.”

Discontiguous megaBLAST =

Another Example . . .

Discontiguous megaBLAST = numerous hits . . .

Query: NM_078651

Drosophila melanogaster CG18582-PA (mbt) mRNA, (3244 bp)

/note= mushroom bodies tiny; synonyms: Pak2, STE20, dPAK2

MegaBLAST = “No significant similarity found.”

Database: nr (nt), Mammalia[orgn]

eEx: Discontiguous MegaBLAST

eEx: BLASTN

PSI-BLAST

Example: Confirming relationships of purine

nucleotide metabolism proteins

Position-specific Iterated BLAST

e>gi|113340|sp|P03958|ADA_MOUSE ADENOSINE DEAMINASE (ADENOSINEMAQTPAFNKPKVELHVHLDGAIKPETILYFGKKRGIALPADTVEELRNIIGMDKPLSLPGFVIAGCREAIKRIAYEFVEMKAKEGVVYVEVRYSPHLLANSKVDPMPWNQTEGDVTPDDVVDEQAFGIKVRSILCCMRHQPSWSLEVLELCKKYNQKTVVAMDLAGDETIEGSSLFPGHVEAYRTVHAGEVGSPEVVREAVDILKTERVGHGYHTIEDEALYNRLLKENMHFEVCPWSSYLTGAVRFKNDKANYSLNTDDPLIFKSTLDTDYQMTKKDMGFTEEEFKRLNINAAKSSFLPEEEKK

PSI-BLAST

0.005 E value cutoff for PSSM

eRESULTS: Initial BLASTP

Same results as protein-protein BLAST; different format

eResults of First PSSM Search

Other purine nucleotide metabolizing enzymes not found by ordinary BLAST

eTenth PSSM Search: Convergence

Just below threshold, another nucleotide metabolism enzyme

Check to add to PSSM

eReverse PSI-BLAST (RPS)-BLAST

eAdenosine/AMP Deaminase Domain

AMP Deaminases

PHI-BLAST

>gi|231729|sp|P30429|CED4_CAEEL CELL DEATH PROTEIN 4MLCEIECRALSTAHTRLIHDFEPRDALTYLEGKNIFTEDHSELISKMSTRLERIANFLRIYRRQASELIDFFNYNNQSHLADFLEDYIDFAINEPDLLRPVVIAPQFSRQMLDRKLLLGNVPKQMTCYIREYHVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQELRLRCLVTTRDVEIASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEK

[GA]xxxxGK[ST]

eGenome BLAST

eGenome BLAST via Map Viewer

eExample Search Pathways:

Hemochromatosis

OMIMOMIM GeneGene

“hemochromatosis”HFE

nucleotide sequence

GenomeBLAST Map Viewer

Protein

Domains

text search

sequence search

eExample: Human Genome BLAST

TGCCTCCTTTGGTGAAGGTGACACATCATGTGACCTCTTCAGTGACCACTCTACGGTGTCGGGCCTTGAACTACTACCCCCAGAACATCACCATGAAGTGGCTGAAGGATAAGCAGCCAATGGATGCCAAGGAGTTCGAACCTAAAGACGTATTGCCCAATGGGGATGGGACCTACCAGGGCTGGATAACCTTGGCTGTACCCCCTGGGGAAGAGC

Human EST

eHuman Genome BLAST: Results

Human Genome BLAST: MapViewer

Entrez GeneEntrez Gene

What’s New?

BLAST DatabasesNucleotide

• refseq_rna = NM_*, XM_*

• refseq_genomic = NC_*, NG_*

• env_nt– environmental sample[filter], e.g., 16S

Protein

• refseq = NP_*, XP_*

• env_nr

eNew Formatter

Select lower case Select red

eNew Formatter

• gray line = same database hit

• hsp’s color-coded independently

BLAST Output: Alignments & Filter

low complexity sequence filtered

eAdvanced Options

Limit to Organism

all[filter] NOT ma

Example Entrez Queriesall[Filter] NOT mammalia[Organism]ray finned fishes[Organism]srcdb refseq[Properties]

Nucleotide only:biomol mrna[Properties]biomol genomic[Properties]

OtherAdvanced–e 10000 expect value-v 2000 descriptions-b 2000alignments

Example Entrez Queriesall[Filter] NOT mammalia[Organism]ray finned fishes[Organism]srcdb refseq[Properties]

Nucleotide only:biomol mrna[Properties]biomol genomic[Properties]

OtherAdvanced–e 10000 expect value-v 2000 descriptions-b 2000alignments

-e 10000 -v 2000

eSearching by Structure

Why search for similar structures?

• Find homologs with low sequence similarity

• Explore protein evolution: similar protein folds can support different functions

• Identify conserved core elements to model related proteins of unknown structure

Why search for similar structures?

• Find homologs with low sequence similarity

• Explore protein evolution: similar protein folds can support different functions

• Identify conserved core elements to model related proteins of unknown structure

Indexing into MMDB

Structure

id 1 , name "helix 1" , type helix , location subgraph residues interval { { molecule-id 1 , from 49 , to 61 } } } ,

Add secondary structure

inter-residue-bonds { { atom-id-1 { molecule-id 1 , residue-id 1 , atom-id 1 } , atom-id-2 { molecule-id 1 , residue-id 2 , atom-id 9 } } ,

Add chemical bonds

• Import only experimentally determined structures• Convert to ASN.1 • Verify sequences

• Create “backbone” model (Cα, P only)• Create single-conformer model

MMDBMolecular Modeling Data Base

Structure Summary

Conserved Domains3D Domain Neighbors

Structure Neighbors

3D Domains

Conserved Domains

VAST: Alignment

For each protein chain,

locate SSEs (secondarystructure elements),

represent SSEs asindividual vectors, 1

Human IL-4

IL-4 &Leptinalign the vectors.

Structure neighbors

Taq DNA polymerase

eVAST Results for the Chain

Table view

Vector Alignment Search Tool

3D Domain structure neighbors

eVAST Results for Domain 1

Not found with Chain query!

Best way to convert PDB files to MMDB format

for viewing with Cn3D!

Best way to convert PDB files to MMDB format

for viewing with Cn3D!

submit file to PDB

eExample: Mapping Oligos Onto

a Genome

>forwardCCATGGCGACCCTGGAAAAGC

>reverseCAGCAGCGGCTGTGCCTGCGG

eMap Oligos Onto Genome

>CCATGGCGACCCTGGAAAAGCNNNNNNNNNNCAGCAGCGGCTGTGCCTGCGG

-W 7 –e 1000

forward primer reverse primer

eGenome BLAST Results

Primer Alignments

forward primer

reverse primer

MapViewer

eSequence View (sv)

forward

reverse

Service Addresses

•BLAST blast-help@ncbi.nlm.nih.gov

•General Help info@ncbi.nlm.nih.gov•Wayne Matten matten@ncbi.nlm.nih.gov

•BLAST blast-help@ncbi.nlm.nih.gov

•General Help info@ncbi.nlm.nih.gov•Wayne Matten matten@ncbi.nlm.nih.gov

ncbi fieldguide a field guide part 2 august 30, 2005 university of colorado health sciences center

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