Twease/FastaTwease

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== Searching biological sequences with information retrieval approaches == == Searching biological sequences with information retrieval approaches ==
 +=== Corpus preparation ===
A version of Twease that can search a corpus made of biological sequences. A version of Twease that can search a corpus made of biological sequences.
I made a corpus with the ensembl human proteins (Homo_sapiens.NCBI36.41.pep.all.fa) and indexed with Textractor/MG4J with overlapping 3-grams as words. I made a corpus with the ensembl human proteins (Homo_sapiens.NCBI36.41.pep.all.fa) and indexed with Textractor/MG4J with overlapping 3-grams as words.
 +=== First sequence query with BM25 ===
Searched this corpus with BM25 scoring and disjunctive queries (i.e., AAP | HIL| ...) and an example query chosen at random among the sequences in the indexed corpus: Searched this corpus with BM25 scoring and disjunctive queries (i.e., AAP | HIL| ...) and an example query chosen at random among the sequences in the indexed corpus:
Line 43: Line 45:
The query sequence is [http://www.ensembl.org/Homo_sapiens/protview?peptide=ENSP00000335566 Keratin-associated protein 21-1] marked as a member of the keratin family (ENSF00000003793). The query sequence is [http://www.ensembl.org/Homo_sapiens/protview?peptide=ENSP00000335566 Keratin-associated protein 21-1] marked as a member of the keratin family (ENSF00000003793).
 +
 +=== Modify the method ===
 +Log inspection indicates that Twease uses only 8 terms in the query (the terms with the lowest corpus frequency). I changed the behavior to include the 100 terms with the lowest corpus frequency. This should help find more matches.
 +
 +=== Next test: TAS1R3 ===
 +The sweet taste receptor should be an interesting test. It has low homology to other GPCRs and human proteins.
 +
 +The following matches are returned:
 +
 + 102 Q0 41031 0 336.1844751538954 twease
 + 102 Q0 41032 1 336.1844751538954 twease
 + 102 Q0 4167 2 53.182348855402594 twease
 + 102 Q0 14048 3 50.04884551615295 twease
 + 102 Q0 2071 4 49.95855069089579 twease
 + 102 Q0 2072 5 49.95855069089579 twease
 + 102 Q0 39985 6 49.741951152235266 twease
 + 102 Q0 5039 7 49.5103894224437 twease
 + 102 Q0 40045 8 48.447158334399354 twease
 + 102 Q0 39904 9 47.41193634057475 twease
 + 102 Q0 39905 10 47.41193634057475 twease
 +
 +Index 41031 is [http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000169962 ENSG00000169962]/ENST00000339381/ENSP00000344411, TAS1R3 itself.
 +
 +Index 4167 is [http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000142449 ENSG00000142449]/ENST00000270509/ENSP00000270509, FBN3 Fibrilin 3. The link is not obvious.
 +
 +Index 14048 is [http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000184613 ENSG00000184613]/ENST00000333837/ENSP00000327988, NELL2, Protein kinase C-binding protein NELL2 precursor (NEL-like protein 2) (Nel-related protein 2)
 +
 +=== With rat TAS1R3 ===
 +
 +Let's check that the rat TAS1R3 finds the human one:
 +
 + 103 Q0 41031 0 147.95588360052815 twease
 + 103 Q0 41032 1 147.95588360052815 twease
 + 103 Q0 21081 2 50.66315874422973 twease
 + 103 Q0 21082 3 50.66315874422973 twease
 + 103 Q0 21083 4 50.257226358209856 twease
 + 103 Q0 40045 5 45.977610216284475 twease
 + 103 Q0 36374 6 44.11439908886646 twease
 + 103 Q0 4962 7 43.908705176987375 twease
 + 103 Q0 32389 8 43.60676044312044 twease
 + 103 Q0 6164 9 43.29170704576298 twease
 +
 +It does, but most of the other matches do not overlap with the initial human search. An exception is sequence at index 40045 (rank 5 in rat search, rank 8 in human search).
 +
 +Index 40045 is [http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000081479 ENSG00000081479], LRP2.
 +
 +LRP2 occured also in previous searches. This strongly suggests that something is wrong.

Revision as of 22:09, 13 October 2006

Contents

Searching biological sequences with information retrieval approaches

Corpus preparation

A version of Twease that can search a corpus made of biological sequences.

I made a corpus with the ensembl human proteins (Homo_sapiens.NCBI36.41.pep.all.fa) and indexed with Textractor/MG4J with overlapping 3-grams as words.

First sequence query with BM25

Searched this corpus with BM25 scoring and disjunctive queries (i.e., AAP | HIL| ...) and an example query chosen at random among the sequences in the indexed corpus:

>ENSP00000331971 pep:known chromosome:NCBI36:21:30774235:30774507:-1 gene:ENSG00 000184351 transcript:ENST00000331764 MSHYGSYYGGLGYSCGGFGGLGYGYGCGCGSFCRRGYGYGSGFGSYGYGSGFGGYGYGSG

At this stage, I could not build a doc store, so the index of the sequence in the input fasta file is used as document identifier (/PMID) in the trec_eval output.

ENSP00000331971 has index 132-1=131 in the input Fasta file (sequence numbers start at 0 with textractor, but grep numbers lines from 1).

 Fabien Campagne@PC120871 /cygdrive/d/dev/ensembl-data
 grep '>' Homo_sapiens.NCBI36.41.pep.all.fa|grep -n ENSP00000331971
 132:>ENSP00000331971 pep:known chromosome:NCBI36:21:30774235:30774507:-1 gene:EN
 SG00000184351 transcript:ENST00000331764

The best matches in trec_eval format are:

 100	Q0	131	0	42.46582283201506	twease
 100	Q0	148	1	28.144966050948458	twease
 100	Q0	133	2	25.34762250828596	twease
 100	Q0	135	3	23.00047774168498	twease
 100	Q0	141	4	22.69864217728251	twease
 100	Q0	134	5	22.67280744193289	twease
 100	Q0	139	6	22.358672780465746	twease
 100	Q0	144	7	22.312434886092404	twease
 100	Q0	132	8	21.778693703352136	twease
 100	Q0	136	9	21.145654858966886	twease

Therefore, the query sequence is found at rank 0 (best). That's a good start. The next best match is the sequence at index 148 in the input file.

 $ grep '>' Homo_sapiens.NCBI36.41.pep.all.fa |head -149 |tail -1
 >ENSP00000335566 pep:known-ccds chromosome:NCBI36:21:31049328:31049567:-1 gene:ENSG00000187005 transcript:ENST00000335093 CCDS13606.1
 Verification: 
 $ grep '>' Homo_sapiens.NCBI36.41.pep.all.fa|grep -n ENSP00000335566
 149:>ENSP00000335566 ...

ENSP00000335566 is a novel gene, but marked as belonging to the keratin family (ENSF00000003793 : KERATIN).

The query sequence is Keratin-associated protein 21-1 marked as a member of the keratin family (ENSF00000003793).

Modify the method

Log inspection indicates that Twease uses only 8 terms in the query (the terms with the lowest corpus frequency). I changed the behavior to include the 100 terms with the lowest corpus frequency. This should help find more matches.

Next test: TAS1R3

The sweet taste receptor should be an interesting test. It has low homology to other GPCRs and human proteins.

The following matches are returned:

 102	Q0	41031	0	336.1844751538954	twease
 102	Q0	41032	1	336.1844751538954	twease
 102	Q0	4167	2	53.182348855402594	twease
 102	Q0	14048	3	50.04884551615295	twease
 102	Q0	2071	4	49.95855069089579	twease
 102	Q0	2072	5	49.95855069089579	twease
 102	Q0	39985	6	49.741951152235266	twease
 102	Q0	5039	7	49.5103894224437	twease
 102	Q0	40045	8	48.447158334399354	twease
 102	Q0	39904	9	47.41193634057475	twease
 102	Q0	39905	10	47.41193634057475	twease

Index 41031 is ENSG00000169962/ENST00000339381/ENSP00000344411, TAS1R3 itself.

Index 4167 is ENSG00000142449/ENST00000270509/ENSP00000270509, FBN3 Fibrilin 3. The link is not obvious.

Index 14048 is ENSG00000184613/ENST00000333837/ENSP00000327988, NELL2, Protein kinase C-binding protein NELL2 precursor (NEL-like protein 2) (Nel-related protein 2)

With rat TAS1R3

Let's check that the rat TAS1R3 finds the human one:

 103	Q0	41031	0	147.95588360052815	twease
 103	Q0	41032	1	147.95588360052815	twease
 103	Q0	21081	2	50.66315874422973	twease
 103	Q0	21082	3	50.66315874422973	twease
 103	Q0	21083	4	50.257226358209856	twease
 103	Q0	40045	5	45.977610216284475	twease
 103	Q0	36374	6	44.11439908886646	twease
 103	Q0	4962	7	43.908705176987375	twease
 103	Q0	32389	8	43.60676044312044	twease
 103	Q0	6164	9	43.29170704576298	twease

It does, but most of the other matches do not overlap with the initial human search. An exception is sequence at index 40045 (rank 5 in rat search, rank 8 in human search).

Index 40045 is ENSG00000081479, LRP2.

LRP2 occured also in previous searches. This strongly suggests that something is wrong.

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