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SetCond

Custom conditions:

Limit

Limit maximum returned lines. The second param can set Offset

Offset

Set offset lines:

GroupBy

OrderBy

Param uses expr

Using - at the beginning of expr stands for order by DESC

Distinct

Same as distinct statement in sql, return only distinct (different) values

RelatedSel

Relational queries. Param uses expr

Count

Return line count based on the current query

Exist

Update

Execute batch updating based on the current query

Atom operation add field:

orm.ColValue supports:

Delete

Execute batch deletion based on the current query

PrepareInsert

Use a prepared statement to increase inserting speed with multiple inserts.

Return the related ResultSet

Param of All supports *[]Type and *[]*Type

All / Values / ValuesList / ValuesFlat will be limited by Limit . 1000 lines by default.

The returned fields can be specified:

The other fields of the object are set to the default value of the field’s type.

Try to return one record

The other fields of the object are set to the default value of the fields’ type.

Values

Return key => value of result set

key is Field name in Model. value type if string.

Return specific fields:

TODO : doesn’t support recursive query. RelatedSel return Values directly

RelatedSel

But it can specify the value needed by expr.

ValuesList

The result set will be stored as a slice

The order of the result is same as the Fields order in the Model definition.

The values are saved as strings.

It can return specific fields by setting expr.

ValuesFlat

Only returns a single values slice of a specific field.

Relational Query

Let’s see how to do a Relational Query by looking at Model Definition

User and Profile is OnToOne relation

Query Profile by known User object:

Cascaded query directly:

Reverse finding Profile by User:

Post and User are ManyToOne relation. i.e.: ForeignKey is User

Query related User by Post.Title:

While RegisterModel, ORM will create reverse relation for Post in User. So it can query directly:

Post and Tag are ManyToMany relation

After setting rel(m2m), ORM will create connecting table automatically.

Query which post used the tag with tag name:

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from the Stephen White laboratory at UC Irvine

When referencing this page, please use this url:
Desperately seeking membrane proteins! CASP13 is now open: Membrane-embedded structures now available!: MPtopo XML data representations now available:

Latest new protein entered: 27 六月 2018 at 20:57 PDT. Last database update: 27 六月 2018 at 20:58 PDT

New Structures:
Unique proteins in database = 799
Coördinate files in database = 2594
Published reports of membrane protein structures in database = 1430
(Counts include pre-publication structures)
A full list of pdb codes currently in the database is available .

include proteins of same type from different species. For example, photosynthetic reaction centers from and are considered unique. Structures of mutagenized versions of proteins already in the database are excluded as unique. Proteins that differ only by substrate bound or by physiological state are also excluded. Structures 'obsoleted' by the PDB are not included.

Total number of PDB coördinate files, including those for unique proteins. This number reflects the fact that published reports of structures often include several coördinate files describing, for example, the protein in different crystal forms, or with different bound substrates.

Pre-Publication Structures
A word about the new interface to the protein table.
Links to the Protein Data Bank Site
Links to the Structural Biology Knowledgebase Site

The table above is initially presented in a collapsed form, and the user can expand different sections of the table, or the entire table, and bookmark different sections of the table, or a fully expanded table version of the page, using the , , , and icons on the left margin of the table section headers.

mpstruc Taxonomic Domain data are derived from the UniProt Knowledgebase , which is based on the Limit Discount Offer Womens Damen Langarm Shirt Mit Stehkragen 3/4 Sleeve LongSleeved Shirt Trigema Clearance Prices Best Place Cheap Online Clearance Shop Offer OASgRL
. These taxa can be searched for using ' Text Search of Table ', above. The following icons are used in the table, as appropriate:

The table provides useful information about integral membrane proteins whose crystallographic, or sometimes NMR or cryo-EM, structures have been determined to a resolution sufficient to identify TM helices of helix-bundle membrane proteins (typically 4 - 4.5Å). Reference is made to all of the protein types whose structures have been determined. We have attempted to make the database as inclusive as possible. If you find errors or omissions, please send a message to Stephen White .

Bombyx mori (Dazao strain) larvae were reared on fresh mulberry leaves in a dedicated silkworm rearing room at ambient temperature (23–27 °C). Genomic DNA samples were separately isolated from virgin female and male individuals with tissue DNA kits (OMEGA, Norcross, GA). In the case of W contigs that had autosomal or Z paralogs, primers for genomic DNA PCR were designed considering the differences between the autosomal or Z paralogs and the W sequence at the 3’ end of the primer. PCR was performed with GO Taq DNA Polymerase (Promega, Madison, WI; Supplementary Table S1–S3 ), RNA was isolated from individual embryos following the traditional Trizol method (Ambion, Carlsbad, CA) using the total RNA isolation protocol according to the manufacturer’s instructions. Residual DNA in samples was used to identify the gender of each embryo with the W_seq1 marker ( Supplementary Table S1 ). Total RNA (following DNase treatment) was subjected to reverse transcription using a PrimeScript TM RT Master Mix (Perfect Real Time; TaKaRa, Kusatsu, Japan) in 50 μl reaction volume (2500 ng total RNA) and then diluted 5-fold. One μg of cDNA was used in 10 μl PCR reaction volume. Small RNAs (following DNase treatment) were subjected to reverse transcription using a Mir-X™ miRNA First-Strand Synthesis Kit (TaKaRa, Kusatsu, Japan). qPCR was performed with SYBR Premix Ex (TaKaRa, Kusatsu, Japan).

Although most of the B. mori W chromosome is composed of TEs whose copies are widely distributed on autosomes or on the Z chromosome, still some subtle variations such as single nucleotide polymorphisms (SNPs) can be observed only on W chromosome. Such W-specific variations may produce W-specific short sequences called k -mers.

For obtaining these possible W-specific k -mers, we tried to find an optimum k value (sequence length). K  = 15, which is a typical value used for filtering errors in short reads, 11 , 19 is suitable for female-specific (W-specific) k -mers in B. mori . We counted the frequencies of each 15-mer separately in female and male sequence data and created a parameter called KQ. For a given k -mer K i, KQ( k i) =  M ( k i)/ F ( k i), where M ( k i) is the frequency of K i in male reads and F ( k i) denotes the frequency of K i in female reads. As females and males share the same complement of autosomes, autosomal 15-mers are present in both female and male sequencing data in roughly the same quantities. Therefore, autosomal 15-mers have KQ values distributed around one ( Fig.1 ). As males have two Z chromosomes while females have only one, the Z-specific 15-mers have KQ values distributed around two. Since unique W chromosomal 15-mers are present only in female sequencing data, these KQ values localize to zero. We also applied KQ to D. melanogaster and An. gambiae [ Fig.1 , exchange M ( k i) and F ( k i) position in XX/XY species]. The results were similar to B. mori , which confirms that KQ may be applied to most sexually heterogametic species.

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