Dealing with Sequence Aliases
The palias view provides a summary of all aliases for a sequence.
It may be used to find the Unison "pseq_id" sequence identifier for an alias,
and it may be used to find all aliases for a pseq_id. Here's an example:
unison=> select * from palias where alias='TNFA_HUMAN';
palias_id | pseq_id | origin_id | alias | descr | tax_id | ref_pseq_id | added
-----------+---------+-----------+------------+---------------------------------------------------------------------------------------------------------------------+--------+-------------+-------------------------------
127210 | 98 | 12 | TNFA_HUMAN | Tumor necrosis factor precursor (TNF-alpha) (Cachectin). | 9606 | | 2003-01-07 14:31:29.751015-08
13498936 | 98 | 10052 | TNFA_HUMAN | Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF-a) (Cachectin) | 9606 | | 2004-09-14 21:14:42.883859-07
(2 rows)
unison=> select * from palias where pseq_id=98;
palias_id | pseq_id | origin_id | alias | descr | tax_id | ref_pseq_id | added
-----------+---------+-----------+----------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------+--------+-------------+-------------------------------
127210 | 98 | 12 | TNFA_HUMAN | Tumor necrosis factor precursor (TNF-alpha) (Cachectin). | 9606 | | 2003-01-07 14:31:29.751015-08
3842651 | 98 | 10012 | gi|20381341|gb|BC028148.1| | Homo sapiens, tumor necrosis factor (TNF superfamily, member 2), clone MGC:39905 IMAGE:5217636, mRNA, complete cds ESTER:CDS:158..859 Path: FC | 9606 | | 2003-01-21 15:44:58.290734-08
5356664 | 98 | 18 | IPI00001671.1 | Tumor necrosis factor precursor; SWISS-PROT:P01375|REFSEQ_NP:NP_000585|TREMBL:Q9UIV3;O43647|REFSEQ_XP:XP_165823;XP_175231;XP_175158|ENSEMBL:ENSP00000229681 | | | 2003-05-02 09:34:49.698736-07
9850526 | 98 | 20 | NP_000585.2 | tumor necrosis factor alpha [Homo sapiens] | 9606 | | 2004-04-20 14:49:25.105249-07
11533537 | 98 | 12 | P01375 | Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF-a) (Cachectin). | 9606 | | 2004-06-04 13:54:28.16476-07
13498936 | 98 | 10052 | TNFA_HUMAN | Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF-a) (Cachectin) | 9606 | | 2004-09-14 21:14:42.883859-07
13498937 | 98 | 10052 | P01375 | Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF-a) (Cachectin) | 9606 | | 2004-09-14 21:14:42.894009-07
(7 rows)
A particularly handy use of the palias table is to self-join on the sequence
identifier in order to map an accession to accessions from other databases.
Here's an example, which sorts by the "annotation preference" associated with
each sequence origin.
unison=> select O2.origin,A2.alias,A2.descr
from palias A1
join palias A2 on A1.pseq_id=A2.pseq_id
join origin O2 on A2.origin_id=O2.origin_id
where A1.alias='TNFB_HUMAN'
order by O2.ann_pref;
origin | alias | descr
----------------------+---------------+------------------------------------ //
UniProtKB/Swiss-Prot | TNFB_HUMAN | Lymphotoxin-alpha precursor (LT-alp //
UniProtKB/Swiss-Prot | P01374 | Lymphotoxin-alpha precursor (LT-alp //
Refseq | NP_000586.2 | lymphotoxin alpha precursor [Homo s //
IPI | IPI00001670.1 | Lymphotoxin-alpha precursor; SWISS- //