Look up SQL Table Value Parameters.
You can create a user-defined table type parameter like:
CREATE TYPE [dbo].[AccessionData] AS TABLE(
[ValueToUse] [varchar](100) NOT NULL
PRIMARY KEY CLUSTERED
(
[ValueToUse] ASC
)WITH (IGNORE_DUP_KEY = OFF)
)
GO
Then in your SQL code do something like:
SELECT a.cluster, b.pig, b.PDBgi, b.PDBaccession, a.Seqstar, a.Seqstp
from clusterPDBpig a
INNER JOIN pig2PDBgi_acc b on (a.pig = b.pig)
INNER JOIN @InputData I on (I.PDBaccession = b.PDBaccession)
Where @InputData is of type AccessionData
The following links provide a bit of information: