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NCBI Molecular Biology Resources
part 2
NCBI
Nov 6, 2001
WWW BLAST
NCBI
Web BLAST
NCBI
Protein Databases
nr
Non-redundant GenBank CDS translations+PDB+
SwissProt+SPupdate+PIR
567,860 sequences; 178,533,065 letters
swissprot
pdb
Non-redundant SwissProt sequences
88,934 sequences; 32,001,993 letters
NCBI
PDB protein sequences
22,726 sequences; 5,068,254 letters
Nucleotide Databases
GenBank+EMBL+DDBJ+PDB sequences
759,631 sequences; 2,714,918,430 letters
dbest
Expressed Sequence Tags (EST Division)
7,309,361 sequences; 3,100,444,103 letters
htgs
High-Throughput Genome Sequences
(HTG Division)
84,374 sequences; 4,355,661,355 letters
NCBI
nr(nt)
Protein BLAST Page
Identifier or sequence
>Mutated in Colon Cancer
IETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESILER
VQQHIESKLLGSNSSRMYFTQTLLPGLAGPSGEMVKSTTSLTSSSTSGSS
DKVYAHQMVRTDSREQKLDAFLQPLSKPLSS
Protein database
NCBI
swissprot
BLAST Formatting Page
NCBI
BLAST Output: Graphic
NCBI
mouse over
BLAST Output: Descriptions
Taxonomy Reports
Sorted by E value
Link to record in Entrez
TaxBLAST
Score
(bits)
Sequences producing significant alignments:
sp|P40692|MLH1_HUMAN
sp|P38920|MLH1_YEAST
sp|P44494|MUTL_HAEIN
sp|P23367|MUTL_ECOLI
sp|P14161|MUTL_SALTY
sp|P49850|MUTL_BACSU
sp|P14160|HEXB_STRPN
sp|P70754|MUTL_AQUPY
sp|P54280|PMS1_SCHPO
sp|O67518|MUTL_AQUAE
sp|P54278|PMS2_HUMAN
sp|P54279|PMS2_MOUSE
sp|P54277|PMS1_HUMAN
sp|P02239|LGB1_LUPLU
sp|P14242|PMS1_YEAST
MUTL PROTEIN HOMOLOG 1 (DNA
MUTL PROTEIN HOMOLOG 1 (DNA
DNA MISMATCH REPAIR PROTEIN
DNA MISMATCH REPAIR PROTEIN
DNA MISMATCH REPAIR PROTEIN
DNA MISMATCH REPAIR PROTEIN
DNA MISMATCH REPAIR PROTEIN
DNA MISMATCH REPAIR PROTEIN
DNA MISMATCH REPAIR PROTEIN
DNA MISMATCH REPAIR PROTEIN
PMS1 PROTEIN HOMOLOG 2 (DNA
PMS1 PROTEIN HOMOLOG 2 (DNA
PMS1 PROTEIN HOMOLOG 1 (DNA
LEGHEMOGLOBIN I
DNA MISMATCH REPAIR PROTEIN
MISMATCH
MISMATCH
MUTL
MUTL
MUTL
MUTL
HEXB
MUTL
PMS1
MUTL
MISMATCH
MISMATCH
MISMATCH
REPAIR...
REPAIR...
2 x 10-68
PMS1
REPAIR...
REPAIR...
REPAIR...
255
67
52
45
43
38
38
36
35
35
33
33
31
28
28
e value cut-off = 10
E
Value
2e-68
2e-11
6e-07
8e-05
2e-04
0.006
0.010
0.031
0.069
0.069
0.20
0.27
1.0
6.8
9.0
TaxBLAST: Taxonomy Reports
Homo sapiens (human)
sp|P40692|MLH1_HUMAN
sp|P54278|PMS2_HUMAN
sp|P54277|PMS1_HUMAN
1459
168
132
0.0
3e-41
2e-30
Saccharomyces cerevisiae (baker's yeast) [fungi] taxid 4932
sp|P38920|MLH1_YEAST MUTL PROTEIN HOMOLOG 1 (DNA MISMATCH ...
sp|P14242|PMS1_YEAST DNA MISMATCH REPAIR PROTEIN PMS1
487
152
5e-137
2e-36
Escherichia coli [enterobacteria] taxid 562
sp|P23367|MUTL_ECOLI DNA MISMATCH REPAIR PROTEIN MUTL
208
3e-53
Haemophilus influenzae [g-proteobacteria] taxid 727
sp|P44494|MUTL_HAEIN DNA MISMATCH REPAIR PROTEIN MUTL
208
4e-53
Salmonella typhimurium [enterobacteria] taxid 602
sp|P14161|MUTL_SALTY DNA MISMATCH REPAIR PROTEIN MUTL
200
9e-51
Streptococcus pneumoniae [low GC Gram+] taxid 1313
sp|P14160|HEXB_STRPN DNA MISMATCH REPAIR PROTEIN HEXB
189
1e-47
Bacillus subtilis [low GC Gram+] taxid 1423
sp|P49850|MUTL_BACSU DNA MISMATCH REPAIR PROTEIN MUTL
187
7e-47
Rickettsia prowazekii [a-proteobacteria] taxid 782
sp|Q9ZC88|MUTL_RICPR DNA MISMATCH REPAIR PROTEIN MUTL
178
3e-44
NCBI
[mammals] taxid 9606
MUTL PROTEIN HOMOLOG 1 (DNA MISMATCH ...
PMS1 PROTEIN HOMOLOG 2 (DNA MISMATCH ...
PMS1 PROTEIN HOMOLOG 1 (DNA MISMATCH ...
BLAST Output: Alignments
>sp|P40692|MLH1_HUMAN MUTL PROTEIN HOMOLOG 1 (DNA MISMATCH REPAIR PROTEIN MLH1)
Length = 756
Score = 255 bits (645), Expect = 2e-68
low complexity
sequence filtered
Identities = 126/140 (90%), Positives = 126/140
(90%)
<alignment edited for brevity>
Query: 61 RMYFTQTLLPGLAGPSGEMVKXXXXXXXXXXXXXXDKVYAHQMVRTDSREQKLDAFLQPL 120
RMYFTQTLLPGLAGPSGEMVK
DKVYAHQMVRTDSREQKLDAFLQPL
Sbjct: 341 RMYFTQTLLPGLAGPSGEMVKSTTSLTSSSTSGSSDKVYAHQMVRTDSREQKLDAFLQPL 400
>sp|P23367|MUTL_ECOLI DNA MISMATCH REPAIR PROTEIN MUTL
Length = 615
Score = 44.5 bits (103), Expect = 8e-05
Identities = 25/59 (42%), Positives = 33/59 (55%), Gaps = 8/59 (13%)
LPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHF-----LHE---ESILERVQQHIESKL 54
L + P
L LEI P VDVNVHP KHEV F
+H+
+ +L +QQ +E+ L
Sbjct: 280 LGADQQPAFVLYLEIDPHQVDVNVHPAKHEVRFHQSRLVHDFIYQGVLSVLQQQLETPL 338
NCBI
Query: 4
Results from nr
Sequences producing significant alignments:
Score
(bits)
E
Value
NCBI
gb|AAA85687.1| (U17857) hMLH1 gene product [Homo sapiens]
238 2e-62
gb|AAA17374.1| (U07418) human homolog of E. coli mutL gene ... 238 2e-62
ref|NP_000240.1| mutL homolog 1 >gi|730028|sp|P40692|MLH1_H... 238 2e-62
gb|AAB38506.1| (U80054) mismatch repair protein [Rattus nor... 217 4e-56
>ref|NP_000240.1| mutL homolog
1
gb|AAF64514.1|AF250844_1
(AF250844)
MutL homolog 1 protein ... 217 4e-56
sp|P40692|MLH1_HUMAN MUTL PROTEIN HOMOLOG 1 (DNA MISMATCH REPAIR PROTEIN MLH1)
gb|AAF59117.1| (AE003838) Mlh1 gene product [Drosophila mel... 129 1e-29
pir||S43085 DNA mismatch repair protein MLH1 - human
gb|AAC19117.1| (AF068257) mutL homolog [Drosophila melanoga... 129 1e-29
gb|AAC50285.1| (U07343) hMLH1 [Homo sapiens]
emb|CAA10163.1|
(AJ012747) MLH1 protein [Arabidopsis thalia...
84 4e-16
gb|AAA82079.1| (U40978) DNA mismatch repair protein homolog [Homo sapiens]
emb|CAB66448.1|
putative
DNA mismatch
repair pro...
73 1e-12
prf||2007430A DNA(AL136536)
mismatch repair
protein
[Homo sapiens]
ref|NP_013890.1|
72 2e-12
Length = MutL
756 homolog, forms a complex with Pms1p a...
gb|AAA16835.1| (U07187) Mlh1p [Saccharomyces cerevisiae]
71 4e-12
sp|P44494|MUTL_HAEIN
DNA Expect
MISMATCH
REPAIR PROTEIN MUTL >gi|1...
55 2e-07
Score = 238 bits (601),
= 2e-62
gb|AAB09596.1|
(U71053)
DNAPositives
mismatch =repair
protein
49 1e-05
Identities = 117/131
(89%),
117/131
(89%) [Thermo...
pir||H72427 DNA mismatch repair protein - Thermotoga mariti...
49 1e-05
Query: 1
IETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESILERVQQHIESKLL 60
IETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESILERVQQHIESKLL
Sbjct: 276 IETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESILERVQQHIESKLL 335
tblastn Results Against ESTs
gb|N32729|N32729 yx75d09.r1 Homo sapiens cDNA clone 267569 5' similar to
SW:MLH1_HUMAN P40692 MUTL PROTEIN HOMOLOG 1 ;.
Length = 537
Score = 221 bits (557), Expect(2) = 4e-60
Identities = 120/146 (82%), Positives = 122/146 (83%), Gaps = 3/146 (2%)
Frame = +3
Query: 384 VRTDSREQKLDAFLQPLSKPLSSQPQAIVTEDKTDISSGRARQQDEEMLELPAPAEVAAK 443
VRTDSREQKLDAFLQPLSKPLSSQPQAIVTEDKTDISSGRARQQDEEMLELPAPAEVAAK
Sbjct: 3
VRTDSREQKLDAFLQPLSKPLSSQPQAIVTEDKTDISSGRARQQDEEMLELPAPAEVAAK 182
Query: 444 NQSLEGDTTKGTSEMSEKRGPTSSNPRKRHRXXXXXXXXXXXXRKEMTAACTPRRRIINL 503
NQSLEGDTTKGTSEMSEKRGPTSSNPRKRHR
RKEMTAACTPRRRIINL
Sbjct: 183 NQSLEGDTTKGTSEMSEKRGPTSSNPRKRHREDSDVEMVEDDSRKEMTAACTPRRRIINL 362
Query: 504 TSVLSL-QEEINEQG--HEVLREMLHNHS 529
T
+ QEEIN G
+
LHNHS
Sbjct: 363 T*CFGVSQEEIN*AGXMRVLPGRXLHNHS 449
Query: 533 CVNPQWALAQHQTKLYLLNTTKL 555
C +P WAL QH T+ L NTTKL
Sbjct: 463 CESPSWALEQHPTQFXLFNTTKL 531
NCBI
Score = 35.2 bits (79), Expect(2) = 4e-60
Identities = 14/23 (60%), Positives = 16/23 (68%)
Frame = +1
Results against PDB - Finding a model template
Sequences producing significant alignments:
pdb|1B62|A
pdb|1BKN|A
pdb|1B63|A
pdb|2GDM|
(bits)
Value
Chain A, Mutl Complexed With Adp
45
Chain A, Crystal Structure Of An N-Terminal 40kd..45
Chain A, Mutl Complexed With Adpnp
43
Leghemoglobin (Oxy) >gi|999936|pdb|1GDJ|
Leg..27
1e-05
1e-05
4e-05
2.0
NCBI
Cn3D BLAST Alignment
Alignment by BLAST 2 Sequences
NCBI
PSI-BLAST
Confirming relationships of purine nucleotide
metabolism proteins
NCBI
PSI BLAST
>gi|113340|sp|P03958|ADA_MOUSE ADENOSINE DEAMINASE (ADENOSINE AMINOH
MAQTPAFNKPKVELHVHLDGAIKPETILYFGKKRGIALPADTVEELRNIIGMDKPLSLPGFLAKFDYY
VIAGCREAIKRIAYEFVEMKAKEGVVYVEVRYSPHLLANSKVDPMPWNQTEGDVTPDDVVDLVNQGLQ
EQAFGIKVRSILCCMRHQPSWSLEVLELCKKYNQKTVVAMDLAGDETIEGSSLFPGHVEAYEGAVKNG
RTVHAGEVGSPEVVREAVDILKTERVGHGYHTIEDEALYNRLLKENMHFEVCPWSSYLTGAWDPKTTH
VRFKNDKANYSLNTDDPLIFKSTLDTDYQMTKKDMGFTEEEFKRLNINAAKSSFLPEEEKKELLERLY
NCBI
PSI RESULTS: Initial BLAST Run
NCBI
First PSSM Search
NCBI
Other purine nucleotide metabolizing enzymes not found by ordinary BLAST
Third PSSM Search: Convergence
Just below threshold, another
nucleotide metabolism enzyme
NCBI
PHI BLAST
>gi|231729|sp|P30429|CED4_CAEEL CELL DEATH PROTEIN 4
MLCEIECRALSTAHTRLIHDFEPRDALTYLEGKNIFTEDHSELISKMSTRLERIANFLRIYRRQASE
LIDFFNYNNQSHLADFLEDYIDFAINEPDLLRPVVIAPQFSRQMLDRKLLLGNVPKQMTCYIREYHV
IKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDI
LKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQELRLRCLVTTRDVEI
ASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEK
[GA]xxxxGK[ST]
NCBI
Conserved Domain Search
NCBI
>gi|7290263|gb|AAF45724.1| CG3954 gene product [alt 2] [Drosop
MSSRRWFHPTISGIEAEKLLQEQGFDGSFLARLSSSNPGAFTLSVRRGNEVTHIKIQNNGDF
FDLYGGEKFATLPELVQYYMENGELKEKNGQAIELKQPLICAEPTTERWFHGNLSGKEAEKL
ILERGKNGSFLVRESQSKPGDFVLSVRTDDKVTHVMIRWQDKKYDVGGGESFGTLSELIDHY
KRNPMVETCGTVVHLRQPFNATRITAAGINARVEQLVKGGFWEEFESLQQDSRDTFSRNEGY
Drosophila Corkscrew CDS
KQENRLKNRYRNILPYDHTRVKLLDVEHSVAGAEYINANYIRLPTDGDLYNMSSSSESLNSS
VPSCPACTAAQTQRNCSNCQLQNKTCVQCAVKSAILPYSNCATCSRKSDSLSKHKRSESSAS
SSPSSGSGSGPGSSGTSGVSSVNGPGTPTNLTSGTAGCLVGLLKRHSNDSSGAVSISMAERE
from genome
CDD Results
Sequences producing significant alignments:
Score
E
(bits) value
3e-63
1e-08
3e-63
4e-13
9e-23
9e-23
1e-18
4e-15
2e-15
1e-13
NCBI
gnl|Pfam|pfam00102 Y_phosphatase, Protein-tyrosine phosphatase
236
gnl|Pfam|pfam00102 Y_phosphatase, Protein-tyrosine phosphatase
55.4
gnl|Smart|DSPc
Dual specificity phosphatase, catalytic domain
236
gnl|Smart|DSPc
Dual specificity phosphatase, catalytic domain
70.2
gnl|Smart|PTPc
Protein tyrosine phosphatase, catalytic domain
102
gnl|Smart|PTPc_DSPcProtein tyrosine phosphatase, catalytic domain, un...102
gnl|Smart|SH2
Src homology 2 domains; Src homology 2 domains bi...88.2
gnl|Smart|SH2
Src homology 2 domains; Src homology 2 domains bind 76.9
gnl|Pfam|pfam00017 SH2, Src homology domain 2
78.0
gnl|Pfam|pfam00017 SH2, Src homology domain 2
71.8
Specialized BLAST Pages
Microbial Genomes
Trace Archive
NCBI
Human Genome
Microbial Genomes BLAST
>APE0122
MVGVFGRLSRHVWVKRWYSILWAPWRMKYIKQAGSREGCVFCEAPSMGDDAKAYNSGHIMVTPYRH
VAELEDLTMDEIVEMAKLVRASVKALKRVYAPHGFNIGVNVPRWRGDSNFMLTVGGTKVIPESLED
TFKKLKPAVEEEARKEGV
Hits to Unfinished Genome
NCBI
Human Genome BLAST
NCBI
>gi|11877232|emb|AJ289857.1|HSA289857 Homo sapiens mRNA for adracalin (ADRACALA
AATCTAGCCCGGGAACCGAGTTGCGGGAGTGCGGTCTGTGCCGTTCCGGCCAGGAGTTTGCCGACTGCAG
ACGTCCTGCGAACCGGCAAGATGTGCTCTCTGGGGTTGTTCCCTCCTCCACCGCCTCGGGGTCAAGTCAC
CCTATATGAGCACAATAACGAGCTGGTGACGGGCAGTAGCTATGAGAGCCCGCCCCCCGACTTCCGGGGC
CAGTGGATCAATCTTCCTGTCCTACAACTGACAAAGGATCCCCTAAAGACCCCTGGAAGGCTGGACCATG
GCACAAGAACTGCCTTCATCCATCACCGGGAGCAAGTGTGGAAGAGATGCATCAACATTTGGCGTGATGT
GGGCCTTTTTGGGGTGCTAAATGAAATTGCAAACTCAGAAGAAGAGGTGTTTGAGTGGGTGAAGACGGCA
TCCGGCTGGGCCCTGGCACTCTGTCGATGGGCCTCTTCCCTCCATGGGTCCCTGTTCCCCCATCTGTCTC
Genomic Context of BLAST Hits
NCBI
Shotgun Reads
NCBI
Trace Archive BLAST - MEGABLAST
>gi|563511|emb|X81593.1|MMFKHN M.musculus mRNA for winged
CAGACGGTCGGAGCTCCTGGCCCCCCAGACCCAGGCCCCCACGCCGACCTGCTTCAC
TTCTTCGAGGCCAGGACTGGGTGATGGTGTCGCTACTCCCTCCGCAGTCTGACGTCA
CACCCGACTGGAGGGCGAACCCCAAGGGGACCTCATGCAGGCTCCGGGCCTCCCAGA
CAGAACAAGCATGCTAACTTCAGCTGCTCGTCGTTTGTGCCTGACGGCCCTCCAGAG
NCBI
Whole Genome Shotgun
NCBI
NCBI Genomic Resources
Microbial Genomes
NCBI
The Draft Human Genome
Microbial Genomes in GenBank
Viruses >650
Archaea
11
Bacteria
50
Eukaryotae 1
Sept. 26 2001
Bacterial Genomes
NCBI
M. tuberculosis Complete Genome
NCBI
Coding Regions
NCBI
Genome Annotations
NCBI
M. tuberculosis vs. E.coli COGS
NCBI
Complex Genomes in GenBank
• Caenorhabditus elegans
• Drosophila melanogaster
• Homo sapiens
• Arabidopsis thaliana
The Human Genome
The NCBI annotation effort
NCBI
The Draft Human Genome
NCBI
Human Genome Resources
LocusLink: a central resource
Human Genome BLAST
Human Maps
UniGene: Expressed Sequences
What Data is Available?

NCBI assembled annotated genomic contigs
•
•
Genome project data
Other primary data
Reference sequences - mRNA, proteins, transcripts

Genome Scan gene models

Mapped variation data

Integrated maps - RH, genetic, cytogenetic, and sequence

Clustered and mapped expressed sequences

Links to outside data sources
NCBI

How to access it?
Resource
Human genome BLAST
LocusLink
Map Viewer
UniGene
NCBI
Type of query
Sequence Similarity
Gene name
Map Location
Database ID
LocusLink
A single query interface to …
UniGene
HomoloGene
PubMed
•Sequences
- RefSeqs
Map Viewer
GenBank
OMIM
Full inositol
report
polyphosphate 1 phosphatase
•Maps – the Human Genome Map
RefSeq
Available for
- RH
Hs
human
- Cytogenetic
GenBank Accessions
Mm
mouse
Rn
rat
-Assembled
Genomic Sequence
Dr
zebrafish
dbSNP
•Genome annotations
Dm
fruit fly
•Entrez links
What is UniGene?
A gene-oriented view of sequence entries
•MegaBlast based automated sequence clustering
•Nonredundant set of gene oriented clusters
•Each cluster a unique gene
•Information on tissue types and map locations
•Includes well-characterized genes and novel ESTs
reagents
http://www.ncbi.nlm.nih.gov/UniGene/
NCBI
•Useful for gene discovery and selection of mapping
EST hits INPP1 mRNA
INPP1 mRNA
NCBI
Hs UniGene Statistics
67,109
1,145,547
1,088,566
+ 631,105
---------2,932,237
mRNAs + gene CDSs
EST, 3'reads
EST, 5'reads
EST, other/unknown
UniGene Build 140
Sept 17th, 2001
total sequences in clusters
20,200
95,289
19,010
sets contain at least one known gene
sets
contain
at least
one EST
80%
uncharacterized
transcripts
sets contain both genes and ESTs
NCBI
Final Number of Clusters (sets)
===============================
96,479 sets total
UniGene Collections Sept 26, 2001
Sequences
Clusters
Animals
human
2,932,237
96,479
Mus musculus
Rattus norvegicus
Danio rerio
Bos taurus
Xenopus laevis
mouse
rat
zebrafish
cow
frog
1,825,043
298,003
56,938
87,310
58,133
89,242
59,265
10,642
7,367
11,984
Plants
Arabidopsis thaliana
Oryzia sativa
Triticum aestivum
Hordeum vulgare
Zea mays
thale cress
rice
wheat
barley
maize (corn)
131,068
47,841
31,826
34,812
69,231
25,997
12,836
2,744
4,041
7,161
NCBI
Homo sapiens
Cluster Hs.32309
Links and Homology
NCBI
Cluster Hs.32309
Mapping Data
NCBI
Cluster Hs.32309
Expression Data
NCBI
Cluster Hs.32309
Sequences
NCBI
Human Genome Map Viewer
SEQUENCE MAPS
•Clone
•Contig
•UniGene (EST)
•GenBank
•GenomeScan
•Gene_Sequence
•STS
•Variation
CYTOGENETIC MAPS
•Ideogram
•FISHClone
•Genes_Cytogenetic
•Mitelman
•Morbid
GENETIC_LINKAGE_MAPS
•Genethon
•Marshfield
RADIATION_HYBRID_MAPS
•GeneMap99_G3
•GeneMap99_GB4
•NCBI_RH
•Stanford_G3
•Whitehead_RH
Fanconi Renal Syndrome
Finding a candidate gene
NCBI
Fanconi Syndrome
D15S182 and D15S143
NCBI
Finding Map Location
D15S182 OR D15S143
ePCR- sequence map
NCBI
Genetic Map
Map Viewer
Display
ePCR results (bp)
Marshfield map (cM)
NCBI
Annotated Genes (bp)
Sequence Maps
Annotated Genes - master
EST hits (UniGene)
Genome Scan models
Genomic contigs
Finding Candidate
Gene
LocusLink
Disease Gene Candidate
Supported by
•EST hits
•Gene predictions
NCBI
LocusLink Entry
But what could it do?
BLink
BLink Results
Hit to yeast
Entrez: Saccharomyces RefSeq Protein
Saccharomyces Genome Database
Yeast Homologue Function
Human Function?
Regulator of membrane pump expression in renal tubules?
Polymorphisms
Mouse Genome Resources - Sequencing
BLAST htgs
Trace Archive
NCBI
Service Addresses
•General Help
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